If you know your max upload speed of your connection, tell bittorrent to not use more than about 80% for upload - if you let it do as it likes, it will saturate your upstream and slow down your download speed due to the way TCP/IP works.

I'd also suggest using a different client, namely utorrent/Azureus/bitcomet (first two are my preferences), since they also make use of encrypted connections to bypass throttling done by some ISPs, either yours or of the person you're downloading from.