Actually, The easiest way to avoid having to try to align the tracks after you import them in cubase is to set them to a fixed length in protools before you export them.
All you have to do is open your protools session, open the edit window and select the cutting tool (just left of the hand tool), then find the track you want to fix and double click on anypart of it in the edit window, this will highlight the entire track including black spots and slince. Now all you have to do is an Alt+Shift+3 for Consolodate Selection and it will consolodate the entire track to one wav (or aiff) file. Do this for each track you want to bring into cubase and you won't have to worry about alignment problems.
btw, before importing protools wav files into cubase I found it neccessary to use wavelab or soundforge to open and save the file to remove the extra information that protools appends to the wav file header. If you don't do this cubase will freak and lock up, it may or may not be the same with the aiff files but I thought I'd mention it.
Hope that helps,