First of all, what Linksys model do you have? I have a Linksys BEFSX41, the most recent firmware version for this model has QoS controls so you can control what apps get priority of your bandwidth. You may be able to do this kind of think in your OS too.
Second, what torrent software are you using? Azureus tends to put most of its traffic on port 6881. Also note that you can (and should) set your bandwidth into the options of your torrent client. For example, if you have 1024 Kibps down and 512 Kibps up bandwidth from your ISP, set those figures (or better yet, slightly below so other web traffic can squeeze through your pipe) into the options of your torrent client.
Good luck. If you answer the above questions, we can help you more.