Milkyway@Home has very little options, in particular to allow one app for CPUs and one for GPUs on the same machine.

Does anyone know of a good guide for setting up the server to have more options for the user so I can pass this on to their admin (who is only a postgrad and doesn't know much about Boinc!)

How about:

https://boinc.berkeley.edu/trac/wiki/ProjectMain

or the main person davea [at] berkeley.edu

https://groups.google.com/a/ssl.berkeley.edu/g/boinc_projects

Thanks! Passed on.