In Premiere, Choose File>New>Sequence. This will give you a brand new timeline, within your project. Put your track matte image in the new sequence and apply all the motion or whatever you want to do with it. Then open up your original Sequence again, and drag Sequence 2 into it from Premiere's browser window.
Or, you could always just add the effects to your matte, then export it as a Huffyuv/Lagarith file, and import it back into Premiere.