Aero position, fit and effort

I've noticed a few things on my first few rides with clip ons and I'm wondering:

- Are your quads supposed to burn more in aero than up on the hoods?
- I feel the need to shift back on the saddle to get comfortable.  Is that a fit issue (I didn't get fir for them) or a lack of flexibility?

I already like aero bars so thanks in advance for the help making it even better.