Set the RF extender in room 1 to CH(0), ID(0) and the RF extender in room 2 to CH(0), ID(1) for example. In the editor for the remote make sure you have dedicated devices for each piece of equipment, preferably hidden IR code devices. For each of these devices simply set the channel and ID accordingly under the Device Properties -> RF tab. I use two RF extenders in my home as well. Works great!

(If you have identical equipment in each room you still need a dedicated device in your configuration file for each. This way you can set each to different RF ID's.)