Just debugged this myself. The code is not very shrewd about idenitfying the clock. It expects the name of the clock (as appearing in the list of clocks) to be $INSTANCE_NAME_theACLK. This is the easiest workaround.
The hard way around that is to modify the code for the SAR to not do the check or to use a different naming convention. The appropriate file to look at is: Program Files\Cypress\PSoC Creator\1.0\PSoC Creator\psoc\content\cycomponentlibrary\CyComponentLibrary.cylib\ADC_SAR_v1_50\Custom\cyadcsarcustomizer.cs. Look at the function VerifyClock() at line 85. I also modified the error reporting on line 103 to report the actual frequency in addition to the range it should be in. The error string is located in cyadcsarcontrol.resx.
Unfortunately, since the instance name is part of the expected clock name, you must have two external clock source if you use two SARs.
At some point, Cypress needs to fix this. In addition, they need to expose the hardware control of the SAR input mux.