Yes, it's possible. Each server will have to have a unique (on your network) machine name, and it's effectively impossible to configure both Remote Access web sites to work at the same time, so if you have PCs you will need remote desktop access to from afar you should join them to the server with RA configured.
You should be given the option, when installing the connector, to join either server. However, you may find that, with both servers running, trying to install the connector you find only the "wrong" server. In that case, shut down the wrong server temporarily; once you've installed the connector on all the computers you want to join to the "right" one, you can restart the other and backups, etc. will be fine.
I'm not on the WHS team, I just post a lot. :)
