A few pointers from our rollout of SharePoint:
If you are going to use the Standard
version of SharePoint, then you will
need to purchase Standard CALs.
If you are going to use the
Enterprise version of SharePoint,
then you will need to purchase both
the Standard and Enterprise CALs. You
can not use the Enterprise CALs
without the Standard CALs.
Also, if you are using SharePoint for Internet facing sites then you can either use CALs or the internet license. If you decide to use CALs then the site must offer some sort of authentication mechanism, however using CALs for a high number of users can become extremely expensive. If you wish to offer the site to a high number of users then the internet license may be worthwhile, although you will need a license per web front end facing the internet.
Edit - Rob, I have just reread your question:
In terms of the managing your licenses, you simply have to enter your standard/enterprise license key (done in Central Admin) and thats it. There is no "Licence Manager" like Terminal Services has to track the number of CALs in use etc. I guess Microsoft are basing this on trust, they trust that you will purchase the required number of CALs for your implementation.
Hope this helps,