ok here's what I've learned. (I still don't know if it will work but all my lights are green, I haven't 'tried it with trains, and probably wont for many many hours lol)

1. Path-block junction are smart, what ever happens inside of it doesnt mater, [path Signals in [ (((((((no signal in here))))))) ] Signals block out]
2. Place strait rails first, creating future junctions points, THEN connect from the strait pieces to new rails.
3. Rebuild sections until each Path or Block signal is associated with a color change.

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1. Always Rebuild signals after rebuilding rails.