This system can be slpit into any number of functional "domains". Each domain would map to specific implementations of the system (as seen in the example list found in Implementation Examples) but which would potentially share the same user base. This means an organisation such as a school could have an ICT helpdesk, a maintenance helpdesk, and a departmental teaching assistance helpdesk all running on the same instance of HelpmeICT. The three helpdesks would share the same user base (i.e. the teachers and staff) but as they are doing fundamentally different jobs they deserve their own domains. Each domain is partitioned so that no information (other than that of users) is transferrable between them, keeping them very seperate entities.
Domains help you have "diversity", that is many different functions housed under the same server. Do not get that confused with scale of implementation. If your helpdesk is simply a very large helpdesk with many different sites, each with their own hierarchy of support agents, then bare in mind that one domain would suffice for your needs. To deal with scale you should read the following chapter and learn about Sites - Scaling the System.