After you have put the first ship in a stable orbit, just use the scenario editor to prep an other one on the runaway at KSC. I suggest you launch on a 90 degrees angle (straight east) on the first one so that it's easy to coordinate launch windows.
Once the second ship is launched, sync orbit, and use each ship's comm's menu (the comm and nav MFD) to put the freq of your choice (by manually changing the frequencey TRANSMITTER, instead of the receiver). You can then fix the first ship transmitter to any freq you like and fix the second ship receiver to that freq, and dock.
I have to figure out how to capture pictures of Orbiter and to put them on the forum... I hope I was useful.