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*.exe won't do you any good in Linux, except if you intend to use wine.
In order to install Bittorrent, I suggest you browse for it through your distro's package manager (If you tell us the distro you're using (use your profile), we could help you a lot better).
Another thing is that bittorrent.com offers downloads for linux, you could download that and just follow the README file.
To be honest you would probably be better with Azureus. It's getting a bit bloated but it's easier to use than a console app. Or you have a look at QtTorrent which is less bloated.
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