Use multi-domians with subdirectory multisite

Hello.

I am pretty far into the setup of my next multisite and came across this, when I were about to install Multi-Domains.

"Please note: Multi-Domains is for sub domain installations only and will not work well for subdirectory installations."

I already installed everything as subdirectory and were hoping to lunch the site next week.. Is there any way to make it work? I was planning to have 1 main domain for the multisite and then 3 or 4 domains to choose from af Pro Site member. Can it work with Subdirectory? If not, how do I fix my problem?

Best Regards,
Rasmus