Lets say I have 1 lvl of witch and then go into paladin and take the eldritch heritage feat to gain a familiar... do my lvls stack to progress my familiar?
no, you use the best of, the witch level is also counted towards 'character level', but it isn't counted twice.
But if I used the beast bonded archetype I could still give it feats and what not correct?
i would say so, that's kind of weird in interactions, but what i wrote before would seem to still be the effective result, you don't count the witch level twice (for itself and for total character level) but either approach (only counting total character level including witch vs. total character level WITHOUT witch + witch level) adds up the same. adding the witch level separately seems necessary to get the beast bonded stuff, and i'm not sure the RAW basis for that approach vs. the other, but i'm not sure what RAW basis there would be to NOT start with the witch familiar bond either. there should probably be a FAQ for eldritch heritage (or similar stacking class features in general) which says that a class level can't be counted twice to stack with itself. i know i've seen paizo staff say essentially that, although i don't think it's in the rules per se.