Not being able to choose where things get installed killed Ninite for me. Their reasoning is "where an app is installed is an implementation detail that users shouldn't worry about."
My SSD can only hold so much, and I don't see the benefit of having a browser or file sharing app on an SSD. That seems like a detail I should care about.
I usually install to the default location.. shutdown the app if running, move the directory, and symlink/mklink the default location to the new location.
This is especially helpful for games/apps you are actively using (on the SSD) but when you're done, or not playing as much, it's still available, just not as fast.
I believe it uses the default Program Files and (x86) directory. Have you tried setting that to your other drive so your Ninite-installed apps default to their, but you can still manually select your SSD for the apps you wish to run more quickly (PhotoShop, etc).
Ninite's ability to group many products into a singular downloadable installer is heaven. Keep up the awesome work.