By default, when using 7-zip, the working directory used to compress the files in is %TEMP%. However this can be problematic, if the compressed file is large (say, 7GB) and the user does not have that much space free on that drive (say, 6GB). This causes the disk to fill, 7-zip to fail to allocate more space. It deletes the temp file and PortableAppsBackup has no explanation for the failure. Such large backups can take over 12 hours, and so this is quite irritating.
Fortunately there is a workaround, which I'm hoping John can incorporate. By passing 7z the -w parameter, the working directory can be changed to the directory where the user wishes to place the final archive. Thus the compression takes place in-place. %TEMP% usually is only needed if the final archive's drive is significantly slower than the %TEMP% drive. Since we are backing up FROM a USB drive, usually one wouldn't back up onto such a drive.
In any event, I think the option should at least be available, and a disk space check definitely needs to be made to alert the user that the archive may fail if the disk runs out of space.
[Edit: I poked at the innards a bit and I see that -w is already passed with %TEMP%. I think that's the default anyways... although the quick help for 7-zip just says it'll use "a temporary directory" which I assume MEANS %TEMP%.]
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Unfortunately, the only way to pass it a specific location other than TEMP or the current drive would be a hard-coded path. Which would kinda default the whole 'portable' thing.
One thing I was considering was having the location of the temp files be the location the user chooses to backup to... so if they chose to backup to %MYDOCUMENTS%\PortableAppsBackup then we'd temporarily create a temp directory in their, use it, then ditch it once the backup is done. But, if the user chooses to backup to the device itself, then the TEMP directory would be used.
Sometimes, the impossible can become possible, if you're awesome!
Is there a way to change the backup directory name on the USB? In place of Documents/ I want to use the name
My Documents/
but the backup only saves the path
Documents/
Are they really going to be anyones documents but your own?
And if someone does use your flash drive, they may naturally think that those out their documents, but they're not. 
Plus, Microsoft dropped the whole 'My' prefix thing in Vista cause they realized it was quite obvious they were really no ones documents but yours.
But in the end, I don't think there really is a way for that at the moment. I can't be sure, I don't use the backup that much.
Try Toucan?