To be honest it's not something you can really answer in a single post, but if you're familiar with how Active Directory groups work and your server is configured to use Windows Authentication (which it normally is in this kind of environment) then setting up permissions is relatively straightforward once you've planned the security model you intend to implement (ie who needs access to what).
I've not used the upsize wizard to create an ADP, but I believe it will try and use Windows Authentication by default. Extend the principles of Active Directory, you create users which go into groups which have permissions assigned to them, into SQL server.
You can, if you really want to, assign individual [SQL Server or AD] logins into SQL server groups, but you might find it easier to maintain group membership at an AD level. So a SQL server group will contain the database/server permissions for an Active Directory group which will contain the AD users. There are some built in groups already within SQL server though you might want to create your own for more easy identification/control over your users.
http://vyaskn.tripod.com/sql_server_security_best_practices.htm
is an interesting articles, you might need to delve past some of the SQL server specific gubbins relatively early in the article to reach the more useful hints and tips, but I believe for SQL server 2000 at least that it provides a reasonable overview into what you should be considering to configure your permissions.
There are loads of articles floating around the place, a quick google search on "SQL Server security" has numerous useful articles on the first page of results alone, but unfortunately it is a bit more involved than clicking a few buttons and you're away.
