But if all psionic classes have there own ML then what of PrC? Are all the powers I use going to be gimp since I started a new manifesting class?
It depends on the prestige class and what the abilites say.
I currently have a psi warrior 7/ elocator 6 in my campaign and I have been counting him as lvl 13 ML. If my elocator was just ML=6 then what is the point of ever picking higher level powers when, by the law of ML> points spent I can never use them? I highly doubt WotC meant for me to only pick lvl 2 powers when they said "+1 to existing manifester class".
For example the elcoator prestige class specifically states
+1 level of existing manifester class
At those levels he gains manifester levels to the existing manifesting class.
Note that the elocator does not always gain manifester levels - specifically he does not gain manifesting levels at 2nd, 5th and 8th levels.
So your psi warrior 7/elocator 6 has a ML of 11 since he does not gain ML for elocator levels 2 and 5.
Before you get all up and alarmed in thinking this "sucks" there are many spellcasting prestige classes that work the exact same way too.
Also spellcasting classes do not stack for CL either so a sorcerer 5/wizard 6 has CL 5 for sorcerer issues and 6 for wizard ones. For certain things (like familiar abilities the two stack, for item creation purposes they do not).