There are several different ways of deploying SEP, using SEPM.
1) Using the deployment wizard. I didn't care much for this option, as I didn't feel that it gave me enough control over the process, although the manuals seem to favor this method.
2) You can create a package and export it. This way allows you to use 3rd party products to deploy.
3) My choice is the find unmanaged tool in the clients section of SEPM. After configuring my deployment policies/templates the exact way that I wanted hem, I found this to give me the most control over what gets installed where.
4) There also seems to be some method of configuring specific packages to be linked to client groups, but I haven't looked much into that yet as #3 has worked fine for me.