I was wondering if saving over the default objects in the editor and customizing them may cause problems when you upload your map to the BBS?

You can edit them any way you like, no problem.

The first two tabs (rooms and objects) are editable
The second two tabs (actors, items) can not be edited, as they are references to internal objects not saved in the level file. You can currently view and modify them by double clicking, but that's a bug; the changes aren't saved or used in this case.