Issa,
Could you provide more information about what you want to do? Are you trying to migrate a domian user to a new system in the same domain, or are you trying to migrate one domain to another?
When you first get into the PCT Template Builder you should have the option to capture the users you want. If you want to capture all users on a domain, specify that you want to capture Domain\*. Once you've done that, configure the template the way you'd like and reference that template when capturing the PCT Package. If you need to migrate the user to another domain you can specify that with the command line switches or in that same interface when you first create the template.
Hope that helps,
Snavebob