Greg,
The frequency is the same, but you will only get the increase in RF performance if you use the MX-800's RF base station (the MRF-200) connected to the IntelliControl's Home Theater IR port via a two conductor wire.
The Intellicontrol doesn't care whether it is actuated by RF or IR. The Niles Code pattern triggers it either way. You can learn the code patterns by hooking an emitter to an IntelliControl MSU, then setting the learning remote in front of the emitter. Every time you press a button on the original Niles RF remote, the MSU will spit out an IR version of it via the emitter. Any good learning remote can learn the codes. When the MSU is in operation it responds to a code sent via the Home Theater IR port or an RF version picked up by the antenna. The MSU doesn't care.
Call me if you have further questions.
Best Regards,
-Eric
Eric Johnson
www.hometheaterpro.com1-800-247-7001