It should be fine as long as you install it into a different dir. However, it probably won't allow you to run both at the same time.
You might also be able to merge them into one if you add the other servers grf files into your ro folder, edit DATA.INI to include the grf from the other server, and edit sclientinfo.xml to have both servers listed, that way you can choose which server to connect to when you start the game. Saves some disk space if you can get it to work. There is a pretty big chance of messing something up however, so if you're not the technical type just install it into a different dir.
Welcome to the server.
My chars: TPC / Tjuven / Dansare / Sinne / Magiker / Byracka / Krigare / Andreas