Maybe others will have better advice for you, but here's mine. I occasionally move games I've installed, from one location to another, but apps and utilities I uninstall and reinstall. Frequently they have alarms, and other features which I figure might get hosed (as GUID said, above) if the registry points to the wrong place.
As to the memo feature, I've never used it. Do you have a "My Documents" folder on your CF? That seems to be the magic wand to get the card to behave the way you need it to. If you instead have gotten the dreaded "Ignore_my_documents" file, then we need to sort that issue out first.
Once you get the My Documents folder, in general you can write to the card just as you can to main, from all of yours apps.
Good luck, and post back with more information, if this is confusing.
