Hi Rohit,
To use the external clock source (SMA connector J201), you do not need to make any modification on the board. It will work as it is.
If you want to use the AD9517 or/and the optional OSC (Y200), you have to make these modifications.
The provided hdl and C drivers are going to work with any kind of setup.
About the modifications, you basically have to solder and remove those resistors and capacitors. If you not familiar with this kind of things, I would recommend to use the external clock setup.
Thanks,
Istvan