Adding motion tracked effects to a complete movie/sequence, on multiple subjects throughout the timeline

Hi all,
I am completely new to After Effects and have just completed my first 15 minute movie in Premier Pro (CS5). This movie is very important to me and encroaching a deadline. I wouldn't reach out with such a beginner question otherwise, so any assistance would be greatly appreciated.
Problem -
I have an exported 15 minute .mov file created in Premier Pro.
I want to apply a liquify effect to a moving target - eg. a person for only parts of the movie.
I can successfully motion track and apply the effect, however when the scene changes within the clip and the person leaves the frame, the motion track continues and the effect is applied throughout the remainder of the footage on everything else that comes into view.
I want the motion track to stop once the body is out of the frame, and then to begin a new motion track later when the body reappears, or when I want to apply an effect to a different object along the timeline.
Have Tried -
Importing my Premier Pro project into After Effects.
Result - The motion track stays on screen from clip to clip, throughout entire sequence
Copy and pasting a short clip in order to add an effect only to the single target.
Result - The motion tracking is greyed out, and if I double click on the clip, it takes me to the entire piece of footage it's cut from, which bring me back to my original problem
Please let me know (from the very basic starting point) how you would do this? Is there any way to stop and start the motion track linearly along the timeline in different positions, and apply different effects?
Thank you in advance.
Ally

Todd's right; without a basic understanding, it's going to be hard to help you.
However, I can try.
Instead of bringing your whole video into AE. Just copy the clip in Premiere that needs the effect and paste it into a composition in AE. Trim your composition so it's just that clip. Follow whatever tutorial you followed to get your effect done (I'm assuming the Demon Face Warp from VCP) and render your video out of AE. Then simply plop that clip over the original clip in your Premiere timeline.
But seriously, you will save yourself much hassle if you go through all the resources Todd linked to. AE is a pretty powerful and complicated program. It's not something you can learn in a day, so charging forward into it will only cause frustration.

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