Yes, all SVTs have the premium sound system with the seperate amp(i think). But that really should not affect that particular HU. Since there is nothing on that HU to connect to the stock HU.
What kind of RF amp do you have? I assume it is a 4 channel?
When you have the fader set in the middle, do both front and rear play or is it only the front?
Describe the wiring...For instance, I assume there are two sets (maybe 3 if you have a sub) of RCAs connecting the HU to the amp.
Let us know and we can help you further.