Before I build templates, I usually run through the process manually via the PCTWizard itself, as you see what options you have right away.
I do not see why you cannot migrate a workgroup user to a domain user, as PCT does have a user mapping feature.
Templates usually allow variables, or at the very least as part of the commandline syntax, so you should opnly require one template as long as it will work on all OSes, so some testing should obviosuly be done first.