The doctrines that nicely arrange how this all works may be worth studying, but I can tell you from experience that God does whatever he wants however he wants and he can do so without contradicting scriptures and without explaining to us what he is doing.
We know from Scripture that regeneration is birth by the Spirit, and there are many indications that this is by the Spirit placing himself within us. Whether at other times there is a filling of the Spirit, though not irrelevant, we need to understand the Spirit does whatever he wants and doesn't need to answer to us. This life is not about us, not even about us understanding him. It is about Him. Even our self-esteeming obedience is not as important as knowing Him (not at all saying that knowing Him can happen without obedience --don't misquote me, but) God is the one putting values on all that happens and what we do. Our assessments not valid, though we must do the best we can --"lean not upon your own understanding", but continue to trust in Him, and watch for the path to have already opened up.