Each tracker maintains its own table of peers, so there is a separate swarm for each tracker. But since they are all working on the same torrent, the peers will work with each other no matter how they find out about each other.
Bittorrent peers trade pieces of files, split up in to pieces where each is validated by a hash. The entire file has a hash as well.
If a peer B receives a piece from peer A, and it validates against the hash of that piece as provided in the Bittorrent file, peer B is happy and doesn't care where peer A got it from.
There's nothing stopping a Bittorrent application from connecting to all available trackers identified in the torrent file and reporting accordingly to all peers on all trackers. You can't have the same piece in transfer from multiple peers, but you can have different pieces in transfer in paralell, and it doesn't matter whether from one or multiple trackers, as long as the Bittorrent application is keeping things straight and not doing something like asking for the same piece from two different peers (which it shouldn't be doing anyway).
Malicious peers are possible, but if all they do is provide bad pieces, they'll fail the SHA-1 hash, and then receiving peers will stop communicating with them. Unless SHA-1 is broken, it's not possible to feed bad data in a torrent. Keep in mind that Bittorrent gives all peers your IP address by design. So if a party wanted to find out your IP they don't have to do anything special. Something like a "malicious" tracker that simply never has any peers is possible, but many Bittorrent applications support DHT which is an alternate, trackerless way to find peers for a torrent. And there is nothing stopping anyone from putting the torrent on another, valid tracker.
Swarm management - the tracker merely tells any connecting peer some IPs of other peers that it saw recently. That's all the tracker does. The peer does the rest including checking in with the tracker and starting communication with other peers and everything else.
How can I join a particular swarm manually in µTorrent?
It's been awhile since I've actually used µTorrent but try right clicking the torrent and looking for options that let you check the trackers it read from the torrent. If you can't do this, you would need to remove the trackers you don't want to use from the .torrent file itself.
If that's not
possible, how does µTorrent decide which swarm to put me in?
I'm not sure. If I happen across this information I'll update this.