If I was going to do things over again, I think I would skip the template and just build my help desk from scratch. I started with the template (one of the Fab40) and thought it was a good plan. I ended up deleting half of it and tweaking the other half. Now I am basically down to one list and a couple of forms. To top it off we are upgrading soon to 2010 and the Fab40 really are not supported by the upgrade. There are ways to make it work, but I am just done. If you are thinking about using SharePoint, here is an easy way to get a simple help desk started.
This is a model you can use if you just want a simple way to keep track of tickets. First you will want to start with a simple list. This is the list that will contain your tickets. Some of the fields you may want to setup for you list are: Ticket#, System/Application, Title, Details, Assigned to, Priority, Customer, Comments, Created Date, Created By, Modified Date, Status, Resolution Date. You probably will want to include the date fields because most likely at some point in time someone will ask you what the turnaround time is on the tickets. If you need help creating a Ticket# you can check this article I wrote on calculating one based on the date.
If you don't care who has access to read or change things on the tickets you are done. If you need to separate the customers and the help desk personnel, you will need to make some more mods. What I did was changed the forms for new, display, and edit to suit these needs using SharePoint Designer. In SharePoint Designer I modified the NewForm.aspx to only show the fields I want the customer to enter. Then I modified the display form to show just the fields I want the customer to view and added an editable comments field. As an easy way to limit access I set up roles for the customers, owners, and customer service rep. I then used the site navigation settings and gave each group a link that is only visible to them. This linked them to a default view which only allowed them to see what I wanted them to see. This is a simplified description of what I did, but hopefully it points you in the right direction so you can get started.