my compound movements.

Ive always been a thin guy, and my weightlifting techniques have always been one of isolation. I have never really incorporated compound basic exercises into my routine as I never really needed size. (I ran track in HS and I box now, so lean and mean is the name of the game).

I feel like my core strength is suffering b/c of avoiding these basics (squat, deads, etc). However I have flat feet, therefore when I squat or dead my knees tend to bow inward to compensate rather than pointing straight out, and I can't help but wonder if this is damaging my body...

Do any of you have any suggestions as to a good workout plan incorporating mass and strength building compound movements without f'in up my knees?

Thanks in advance!