Many programs will inform you when you install that it needs to go into main memory. Some will still go into main memory even if you tell it to go to the storage card.
As previously stated, programs that are used upon startup and that are in your startup directory should always be in main memory, and data on the storage card.
I would suggest you download "Advanced Configuration Tool" [available here
http://www.freewarepocketpc.net/ppc-...tion-tool.html] and change default locations for things like download files, IE cache, cookies, history; and anything you can to storage card.
Bottom line is to keep as much main memory free as possible.