DAPUNISHER, first welcome to the team! Are your machines running 24/7?
I don't use the CLI version, so I will have to let others help you configure the team number, but I can help with your question about the GROMACS core.
There is nothing special you need to do to get a particular core. When your client requests a work unit from the F@H servers the client will check whether the appropriate core is available on your machine and if not it will be automatically downloaded. Various proteins need various cores, and core updates come out every so often, so you can end up with multiple EXEs in your F@H directory. There is no way to control which work units you will get assigned, but it does seem that if you use -advmethods you are much more likely to get a GROMACS WU.
My GUI version looks like this:
"C:\Program Files\Folding@Home\winFAH.exe" -advmethods
If you can stay logged on 24/7 you might as well run the GUI version, it sounds easier to configure (there is a dialog box to put in the team number, for example).
Anyway, look forward to you popping up on the team stats!