You should avoid the Popup class. At a recent PDC, they said it wasn't hardware acceleration or anything else. I would place a Canvas or Grid or a combo from both at the bottom of the page (so it's on top, but you can also set the Z-order) and translate it from the screen. Then revive it. Look at minimizing the control if it is not in use, if you are having problems changing its layout or using resources.
Myself, since I have several years under my belt, I would write a new control and use the part and state model to switch it on and off, etc., but if you are new to Silverlight, then this may be the head bank.
Silverlight, Karen Corby MIX08 . , http://videos.visitmix.com/
http://videos.visitmix.com/MIX08/T20