Hi Cien,
I am just a little confused now. In one of your first posts you said that the evaluation board was working fine in the default configuration. Has something changed? Did you make sure to adjust the DCO delay timing as described in the User Guide. The board setup procedure begins on page 6 and details what you need to do. It appears that the timing is just misaligned in your plot above.
I spent some time and configured a board in the manner you originally requested (using the OSC_IN input of the AD9523). I did not have a 50MHz crystal but used a 122.88MHz crystal to verify the procedure. I have attached an mgp file that should work for you.
I would recommend to keep two instances of SPIController open, one for the AD9643 and one for the AD9523, so you can write to each device.
I would like to let you know that I will be out for the Christmas and New Year's holidays after today and will not return until January 13th. I believe this should get things running for you though.
You will also need to save (and overwrite) the AD9523 cal file on your PC. Please copy the attached .cal file into your C:\ProgramData\Analog Devices\SPIController\Cfgs folder. You will need this to write the registers in the AD9523, if you do not use this file then SPIController will not write all the registers on the AD9523.
Regards,
Jonathan