Dear Victor,
The reference C application can setup the chipset for either internal and external clock mode, this is decided by the fourth argument passed to FMC160App.exe. The first thing you wanna do is to get FMC160App to operate with your external clock. The design should work the same for external and internal clock, assuming the external clock is 1800MHz (+8dBm). You will also need to look into the clock tree settings to maybe divide your clock differently, etc.
Then you will want to create a list of the required register read/write the software is doing through sipif_writesipregsiter.
Finally you want to replace sip_mac_engine in the firmware with a state machine pushing the value at given addresses the same as the firmware did.
Bottom line, it wont be as simple as writing 1100 in a register to get 1.1Ghz sampling rate, the chip set is rather complex
Best Regards,
Arnaud