Yes, the secure connection is indeed supported throughout CloverDX. You can get the idea in two documentation pages that describe a secure connection between CloverDX Designer and Server. The first page describes a situation where the Designer (or generally client) has its own certificate: https://doc.cloverdx.com/latest/designer/designer-with-certificate.html
and the other page is related to setups when you don't need the client to have its own certificate:https://doc.cloverdx.com/latest/designer/designer-without-certificate.html
Please review and if you need a more detailed description, please provide me with more details about your use case:
1. Which one of the above mentioned is what you need to achieve (the client has its own certificate or not?)
2. By "system database", do you mean the DB where CloverDX Server has its files? Or do you mean a DB you are accessing with Designer components? Or both?
I know that configuring SSL might be tricky, therefore please let me know the details in case any difficulty or question arises during the process and I'll be happy to help. Have a nice day, Eva