We currently have 2 95 and 1 98 PC running on our network as well as having several 98 users dial in.
The users use there own accounts as normal, the computers are set up on the domain from the individual PC with the computer created on the domain by the Administrators account and password (Right click neighborhood network etc. The only thing you need to do that is OS specific is to ensure that netBEUI is installed else you can't browse the network easily.
Setting up from the server is a nice idea if you have lots of computers to do in one go, but in practice you can't beat sitting in front of the PC and configuring from there, after all the Server is working, it's only the PC that can't see the server and network!