Generally the data sheet for the encoder will specify which signal leads which.
For example, it may say... A leads B in a clockwise rotation.
So if it's turning clockwise then A will come first followed by B. Conversely if it's turning counter clockwise the B will come first followed by A.
I highly recommend downloading and reading this excellent white paper on quadrature encoders. It explains the A versus B, and provides mostly functional code. The sample code does have 2 bugs, but you should be able to find them. If not PM me. Our team has been using this methodology for the last 2 or 3 seasons very successfully.
http://www.chiefdelphi.com/media/papers/1490
Read it, I think you will see the lights go on in your head and you'll have a much better understanding.