If the client asks to 'merge', it means that the torrent is the same (hash) on both trackers.
ATTENTION: Merging will result in the client to mix upload and download from peers of both tracker together. This will result in wrong UL and DL reported to both tracker!
Which exposes a member to getting in trouble for cheating on both tracker.
In your own interest, do that only with public torrents.
Only if the two torrents appear separated, one for each tracker, you are save.
A solution on same torrent is to run two different (instances of) clients.