Domain mapping & SSL

I am using sub-folders (so sites are like, etc) for multisite.

I want to use domain mapping to map TLDs to site1, site2 and so on. The challenge I have is that my SSLs are installed from WHM, not cPanel. As I understand it, I don’t set up TLDs to be mapped in WHM but as an Alias in cPanel. Therefore, the TLD being mapped to site1, site2 ect aren’t picking up the SSL.

Is there a solution for this?

Thank you,