Ok so my problem is when i get a pair and sometimes when the corners aren't fliped right i do a (R,U,Ri,Ui) is this ok, or should i try to stop this all together.
Hmm. I don't get what you're asking. If I invert that (U R U' R'), and then run it on a solved cube, I get one of the simplest F2L cases, that only requires R U R' to solve it. The U' is extraneous (unnecessary to solve the pair). The R U R' sequence is the most efficient for that particular F2L case.
So what's your question?
Brian.