You can change the default length of the project from 120 frames to whatever you like in the Preferences.
If you have a compositor that has a tracker, that may be the best way to track the eyes. If not, you'll have to manually match them up. When doing it manually I find it best first to move the emitter into place every 5 or 10 frames first, and then adding more inbetween keyframes as needed.
1. How do you tell beforehand how many frames the clips has as it is always preset to 120?
Depends on your Frames per Second. But basically, if your footage is 30 FPS, 10 seconds of video would be 300 frames.
However, pIllusion can check this for you. In the open footage dialog, on the right side, under the image of your movies first frame, it tells you how many frames it is.
Also when you import it, in the BG image options dialog, it will tell you what the last frame number is. in addition, if for some reason you still don;t know how many frames it is, just scroll down in the timeline until your footage stops. That's how many frames it is.
If you know your FPS, you can set pIllusion to use the same FPS in the project settings. (View > Project settings).