I am pumping to feed my baby breast milk but also using formula. (i'm not producing enough). Should I do breast milk only and formula only bottles?

I would. I don't have science behind this, but i don't know if mixing breast milk and formula will break down the good proteins in either liquid. I'm probably being overly cautious with this recommendation. So, if it was my baby, i wouldn't mix. Hope that helps!
Shouldn't matter. If i'm understanding your question correctly: can you use the same bottles for both breast milk and formula? Then the answer is yes. As long as you wash them between uses, you can use the same bottle for breast milk and formula. You can even mix the two together!