Unfortunately, there's no solution for that. The problem is that, when you edit any file on the torrent content, it doesn't correspond to the torrent's hash. Effectively, the programme thinks it's a different file, which it kind of is once it's edited in any way. Only 2 things you can do if you want to seed is a) leave all content from your active torrents list completely untouched - it's what I do although my perfectionist ocd is killing me, I'm in the same position as you, only I use JRiver Media Centre - or b) reserve space somewhere on your drives to keep all your torrent content and then copy it to where you'd normally keep it, which means you'll end up with double the space for the same stuff.
Both of those options kinda suck, I know but hey, we're getting free stuff. We might as well put in a little effort, right?