Didn't notice that the OP also asked about backing up from a clean install...
I just did this yesterday, going from an Aosp rom to a Sense rom...
After doing your install, and getting what apps and settings taken care of that you want, go into TB and do a batch backup of both the apps and the system settings.
I've never really used the system settings backups, other than wifi info, but I just like to have the backup'd settings for just in case moments.
I also will clean out my backups from time to time, doing a complete delete of the backups. But before I do this, I make a copy of my TB sd card folder and place it into a folder on my notebook for safe keeping in case I ever need it. Never needed it yet, but you never know...
Team Eos 3