Usually this is catered to midi. The recorded info is set to a particular resolution and by quantizing, you're able to correct anything within the score so that it's falling in time with the other tracks or it gives you a certain feel or flow. This does'nt work for audio files. The equivalent for audio would be time strecthing/compression.

I am familiar with track delay in the Sonar environment. Do I line up the beginning's of each wave file or try to match peaks? Should I phase flip? I guess I'm looking for a confirmation as to whether or not I'm doing correctly.

Well, I'd try lining up the tracks then using each tracks advancing/delay option to get them sync'd together. I don't know of any other way to accomplish this at the moment.