Regardless of what warping method you use, I usually recommend that you get the Start Marker placed at the first clear downbeat of the audio before you start warping.
This means that you’ll be leaving out any intro material from the clip. In order to have that material play back, once the clip is warped, you need to move the Start Marker back into the negative numbers:
The problem in the above example is that the Start Marker is now located somewhere in the middle of a bar:
This means it won’t line up with other clips properly. For conventional tempo-based music in which you want everything to come together “on the one,” you’ll generally want to pull the start marker back to the beginning of a full bar: