I've not used AppManager, but one of its intentions is to let you regress to a previous version of an app you may have backed up in the event that a later version is somehow borked.
You won't end up with installed duplicates.
I use other backup apps that seem quite similar and have the same concern but with overwriting the backups.
In my case, I simply keep folder called EVO_backups on my laptop, and under that are folders named by dates, and within each is a copy/paste snapshot of my SD card. That way, no matter what the apps do - right down to the backup program changing - I can go back to any point in time with my apps and I don't worry about what the phone thinks is latest and greatest.
Hope that helps.