Refuge sums up the whole path and it gets deeper in meaning as one progresses.
One doesn't start by taking refuge in oneself, since what we know about ourselves when we start the path is exactly what we take refuge from.
So first we have the outer level of refuge. From a never ending cycle of suffering, we take refuge in the Buddha, his teachings and those practicing them. This is the outer level of refuge. It's closely related to the understanding of the 4 Noble Truths. You see Duhkha, its causes, hypothesize a state beyond Duhkha attained by the Buddha and, to realize it yourself you follow the teachings helped by those who already do it. Seems wise.
This is how one starts. One doesn't immediately start taking refuge in Buddhanature (even if one does so in fact, one doesn't realize it properly), as one has no clue about it. With practice Dharma becomes more experiential, going deeper than a simple intellectual understanding. Depending on the tradition the practice changes a bit. For instance, a practitioner of Dzogchen, while remaining in the recognition of rigpa, is always in refuge.
Practically speaking, taking refuge is not simply something one recites. It sets the right tone for formal practice, but it doesn't end there. Taking refuge is living according to Buddhadharma, meaning living mindfully and not getting distracted while having a correct view (the absence of views always translates itself as having a view when we act, e.g. not harming others). So in a way, taking refuge is both the beginning and the whole of the practice, formal and not formal. Taking refuge is living accordingly to the teachings, teachings that we understand deeper and deeper the more we practice, and that is being a Buddhist.
In a nutshell, that's about it.
Now, if you allow me the indiscretion, why do you ask? What is more important is knowing what the Three Jewels mean to to you. From what I've read in the thread, seems to me you have some good ideas about refuge, but you need to clarify them (to yourself) a little better. Taking refuge in "oneself" may be read differently. If you mean taking refuge in your own Buddha nature that's fine, but if by oneself you mean the aggregates, then you head to trouble.
I hope my answer was to your satisfaction.