WHMCS is a good billing system, but they are less focused on their support features. Instead use software dedicated at being the best support help desk possible, with a superior feature set, powerful interface and overall better experience for both users and operators.
If you're running multiple WHMCS installations, each can be connected to the same SupportPal installation. Each integration can be set to a specific brand if you wish to separate the tickets, departments and self-service content between each WHMCS installation.
Keep SupportPal and WHMCS in sync, the integration will automatically send any new and updated user accounts in WHMCS to SupportPal so the same information is stored on both ends.
When a user creates a ticket at your client area, they'll have an option to select a related product/service, a dropdown populated with all their products from WHMCS. This product is then highlighted in the operator ticket view.
Many users may be asking questions that can be easily answered with pre-written articles. Have the option to show users related knowledgebase articles when they're submitting a ticket.