Stuart,
You're welcome.
1) Yes, if you find the custom map menu in the GPS you can toggle them on and off, if they are in separate files. Things get screwy if the sum of all the files is greater than the tile limit (100 for many units).
2) You can display GPX files unders "tracks..." on your GPS on top of the custom maps, if that's what you are asking. Active log will show up on it, too. If you want permanent changes to the map tiles, you'll need to regenerate the maps in TF with new tracks.
Regards,
Scott