The only suggestion that I could make with regard to improving the backup tool would be that you might consider adding an option to sync the Application Settings and Favorites directories. This would save some steps when restoring, but wouldn't necessarily be useful for everyone.
If you keep your SmartFTP profile in a non-standard location and you're doing a restore, you have to navigate to the place you want it. Then -- presuming that you're not keeping your SFTP Favorites somewhere else entirely -- you have to navigate back to the same location (however many steps that might be) to set the Favorites. If there was a button to automatically fill the path (possibly with an appended "Favorites" directory at the end of the path) that would be quite slick.
Alternatively, you could simply cut and paste the path from one location field into the next field, and then modify it.
This would be the ultimate in userfriendliness, but I hardly think that anyone would complain about the functionality as it currently stands.
There is something that I noticed about the behavior of... I'm not sure if this is the backup tool or not, but when I did a backup and reset, I watched my profile data on the remote drive get deleted. I happened to later take a look at the default profile directory -- C:\Documents and Settings\Administrator\Application Data\SmartFTP\Client 2.0 -- and I noticed that there are still what looks to be a full set of default Favorites and settings files in that directory.
I guess it makes sense that the backup tool would create the settings for a default profile if you cleared out a previously established custom profile. However, when I did the restore of my custom profile, this alternate/default profile was left intact while the custom one was restored and set in the UI. There's a potential problem in the leaving of profile fragments, both in terms of confusing users who might be hunting around and stumble across it, and also in terms of possibly leaving passwords or other security data where you don't intend to.
I'm not sure if this is the best idea, but it seems like it would be a good idea to only have one set of profile data, and that during a restore, there should be some kind of option -- like the "reset" during backup -- which would have the utility clear out previous profile data so that there's only ever one set of profile data on a system.