If you mix up between going into prep and not going into prep (especially if they have great answers to it), are able to CH confirm Prep BB for the BE, know spacing of opponent's moves and how to evade them, delay moves effectively in prep and SE to mess up step-attack timing or hit TCs, have the ability to make the hardest of reads... then you can make Prep work. Prep is like playing a character with no fast safe mid or the ability to step or guard but with an aGIing backstep, insane TC, insane CH tool, and you have to be able to do everything well to make it worth it. I just described a low tier character...
Anyway, with Raph, you should focus on the neutral game, taking advantage of his speed and range, and try not to play any clear guessing games, because the risk/reward just isn't in your favor. That means delay all your attacks, shorten strings, and know frames/ranges where 6BB will stuff them at disadvantage. They must never know the timing of when you're going to attack or try a low or whatever. Prep comes in when you bait stray whiffs and punish with 3(B) Prep B(B)*A(B) or when you chance a 66(B) or 44A(B), or when using spaced 3B and 6BB as a zoning tool, sometimes going into prep and sometimes not. It's never something you going into for the sake of going into.