Assuming both OSes are a Windows variant, sure. Install the agent on the second partition just like you did the first. When you run it the first time you'll see the registration dialog. Check the box to indicate you are already a member and enter your current member name and password. That's it. When you log into the member area of the site, you will now see two devices, one for each agent install. Both agents are separate and will work on separate work units.

If instead you want to work on the same work unit on either OS, you would have to install the agent on a shared partition, so you could run it from either OS.