Include system items/data in folder organizer label (for backup purposes)?

I use Folder Organizer to group/label a baseline set of apps+data for Titanium to backup - for switching roms, etc. It works great but there are a couple of things I haven't been able to figure out (if they're even possible).

1. Folder Organizer doesn't see Beautiful Widgets or Swype. So, I can't add them to a category. I guess they're not classified as apps by the system.

2. I can't figure out a way to label "System Service" items that have useful data (MMS, wifi, etc). This one may be outside the scope of Folder Organizer though.

It's not hard to just backup the few things that aren't labeled individually but I'd like to get it all down to one step lol.