You can actually mark in and out point just like Premiere before you bring the clips to your comp.
The easiest however is to do the edit in Premiere, right click on the clip and choose replace with After Effect Comp. That will create an After Effects Comp with the right settings and the length of the clip in your timeline.
The best part is that it becomes a dynamic clip, so you don't have to render in After Effect to see the changes in Premiere. (although you will probably have to render in Premere to see real time).
If you are doing a lot of these, I would actually advise rendering a file out of After Effects, since many dynamic links can really slow things down.
Vince Becquiot
Kaptis Studios
San Francisco - Bay Area