I created a template and filled out the proper fields but Category and Sub-category don't show up when a self service user tries to log a ticket.
Is there a reason why?
In the the design of the template, the customer had a service value of "Clinical Application" listed.
If you go to the application logged in as Administrator account and open the CI.Service workspace, select the Clinical Application Service, then click on the "Service Desk Category" tab, does the value exist there as Linked? If they do not you can add them to the Clinical Application service from the CI.Service workspace simply by clicking the Link command button on that CI.Service. If they do not show when linking, then you can add New Categories here as well.
As for Subcategory, those are listed in the PickList in AdminUI named "SubCategory by Service and Category".