As a starter for discussing a generic framework of working hypotheses, I have reframed some old ideas of several theosophies into a modern form, a process-theosophy, including some pertinent scientific concepts. A part of this comes from a heavily reframed  original article of mine: (see the part December 4: the seven jewels of wisdom). It is a panentheistic framework, holding to the philosophical position of objective idealism, not unlike the evolutionist process philosopher Charles Saunders Peirce.

Here goes:

Some principles for a holistic philosophy of life

1. We live in an energy world. Matter is convertible to energy and light. Briefly stated: thoughts are energy-patterns; feelings are energy-patterns; action is of an energetic nature. Consciousness is activity in substance (perhaps identical to the perceptive process). And so on. Life is a process within this energy world. The role of substance and consciousness is to be researched much more in-depth, as it [they] play(s) a pivotal role in all these statements. The principles formulated here are directed to bio-psychological and social processes, including spiritual factors, and the modeling of these processes.
The term “energy world” is borrowed from Vitvan, who has developed a modern gnosis after World-War II. My ebook contains more info on him. He includes the notion of dynamis (dunamis), power, from Aristoteles and Neo-Platonism. That power underlies energy (energeia - dunamis in action, expressed in some field of action). Many great teachers have incorporated this notion in their teachings. It is indispensable for the inclusion of spiritual factors in this framework. “Laws of nature” are seen as habits of nature, formed in evolutionary processes (cf. Peirce).

2. There are interactions between organisms and their environment (other organisms and entities). The coupling between organism and environment gives rise to feedback-loops (mutual influences). Organisms are learning, developing, systems. Flows and cycles are a natural and ubiquitous phenomenon. In ancient philosophy and religion, this feedback is sometimes called karma (action and reaction, also working on the moral level of being). Experience and perception are central to life. Self-organization, autopoiesis (“self-making”) and adaptivity are core features of organisms. (As to minerals: the Neo-Platonic philosopher Proclus says that stones have being, but are not an "animal" (self-moving)). In this framework, all beings are in some sense “alive”. We don't recognize so-called “dead matter”. That would lead to false dichotomies such as the “mind-body” problem, and an absolute separation of matter and spirit. There is no such problem, since all is process, of a substantive nature.

3. Organisms are composite, complex systems. There is a control-hierarchy to steer processes within the organism, as well as between an organism and its environment. An example of a theory that deals with control and viable systems, is the management cybernetics of Stafford Beer. It is widely applicable, also to organisms.

4. All entities have their unique, substantive pattern, based upon which they manifest, develop, grow, and die. This pattern, or archetype, or paradigma, is the basis of inner identity (self), autonomy, sense of freedom and sense of morality. The expression of all this in the world is influenced by the environment. There is inherent unpredictability in the natural world. Since there is free will and choice, the outcome of actions cannot be predicted precisely. This has led the philosopher J.G. Bennett to introduce the concept of hazard. This does not mean that life is a haphazard process. There are patterns being manifested all of the time.

5. Evolution is the process of gradual development (unfolding) of capabilities, latent within each being. There are multiple evolutions (physical, mental, spiritual) going on. Kingdoms of nature show jumps in qualities developed. This is related to the foregoing postulates. Adaptivity is a core notion that can bridge the perceived gap between science and spirituality, if taken as an ability (faculty, aspect of a power) of organisms to actively adapt itself to changes or actively change the environment they live in. Lastly, evolution is concurrent with involution as a process. These two are intertwined. To use a popular phrase: Spirit wraps itself in matter - involution of spirit and evolution of matter – otherwise called the arc of involution; then there is the arc of evolution of spirit (and etherialization or involution of matter). Compare the soft flesh of the animal body with the hard stone of rock to get a glimpse of the latter idea.
These notions are to be found in some form in many religions and philosophies: from the Neo-Platonic “abide, proceed, return”, Theosophy's version, to Alfred North Whitehead's process-philosophy. The incarnation and the ascent theme.
A related matter is that of the existence of subtle realms or spheres of being. Experience teaches us that these exist indeed. How much this notion will be incorporated into models depends on the model in question and the level of detail of description. It might be opportune to work with so-called “black-boxes”, where we leave the exact working of a process undescribed, mostly because of the fact that we don't know how certain processes or subsystems work. This technique is used very often in operational research and cybernetic  management science. Stafford Beer must be mentioned again here.

6. Manifestation is based on the principle of polarity/duality.

The regulative consciousness-principle works through associated flows of energy-matter and associated configurations of energy-matter.

Some examples are: psychosomatic diseases; light-matter coupling (boson-fermion); male-female attraction; electromagnetism; antagonisms, as in how muscles work and countless other physical 'mechanisms' do; complementarity; particle-wave duality; opening a tap to fill a glass with water. The “pairs of opposites” is a familiar notion in the Bhagavad Gita.

7. There is a unified “field” or "matrix" of substantive consciousness, from which emerges 'wave-particles' of consciousness-energy-matter, variously called life-atoms, monads, souls, etc., that share in the properties of this field, in their own appropriate way, by having their own, limited, characteristic pattern or “energetic signature”. This “field” is the basis for connectedness and interaction. It can be called a Source. Behind such a Source (of which there are countless ones) there is the Transcendent, about which nothing can be said, except in the way of negation.  
As to the Matrix mentioned: an analogy with the quantum field (vacuum) from which arise (virtual) particles could perhaps be useful to some degree. Light-particle interactions come to mind too in this connection.
The notion of a Matrix (“Mother” Space) is a very familiar one, both in esoterism as in biology (in its own way). Jacob Boehme frequently uses the word in his intuitive writings.

8. Our notions of time are weird, as some philosophers have noted. Instead of a unidirectional “arrow of time”, we have to include another sense of time, phrased here as the influence of future events on the now. As the past is a living memory in us, so is the future always with us, potentially, and in another form, actually. The working of mind has been described aptly in this respect by J.G. Bennett in his tome “The Dramatic Universe”. Especially see his notions of hyparxis, “ableness-to-be”, and “eternal pattern”, the greater-present-moment, and the role of commitment and decision. These are intuitive concepts!

9. Some modelling has been done by me in the integrative philosophy blog postings and creation philosophy model (postings 1-5, on scribd in one PDF). This is a preliminary work, like the generic framework above, and related to it. Many conceptual models (related to experience) will be possible. Related to this framework, however, they will all start from or include a spiritual point of view, in contradistinction to the physicalist/materialist view.
So, we have a generic framework first, outlining some basic principles of our philosophy; then a generic conceptual model of process  (described in integrative philosophy blog post #1), fitting in this framework, and based on more detailed knowledge and experience of process. Finally we have specific conceptual models, such as for the psychological creative process and other processes. Value systems and organizational components play an important role in all these models. Other generic conceptual models can be formulated as well, or existing ones can be refined. That's all in the nature of investigation and experience.  We have to start somewhere. The generic framework can be and will be extended as well.