ssl or ucc certificate with multisite (subdirectories)?

Hey! I’ve been trying to find a good resource on this, but have yet to come across one.

I currently have a multisite subdirectories network. I let users sign up and open up their own site where they can sell stuff with marketpress.

What is the best way to get this configuration all secured?

The answer should be scalable as I don’t want to run into a major issue if the network starts accumulating sites, let’s say the hundreds or thousands (being hopeful).

Also, the security should be in effect immediately. If a user signs up, they should not have to wait days for the security of their site to be in effect.

Lastly, I offer domain mapping, so not sure if this affects security certificate