To do this, you can expand the data set in the workspace tree so that you can see the channels within it. Hold down Ctrl and select the channels on which you would like to perform a RMS by clicking them, then right click and choose Calculations->RMS. In the RMS window, the Applies To section will list these channels.
To plot the processed channels in conjunction with the unprocessed channels, expand the RMS calculation as well. Then Ctrl-click to select the processed channels from one data set and the unprocessed channels from the original data set. You can then right click and choose Plot. (This operation can also be done within the Plot->Create Plot wizard.)