By "migration host" do you mean the application named "Migration Assistant"?
On the Mini, which drive is the boot drive?
I'm assuming the SSD, is this correct?
Although you can select different source drives (the drive you're trying to migrate from), I believe that the Migration Assistant app assumes that you want to migrate all your data to the boot drive.
I'm not sure if there's any way to change this within the app.
If you have some data that you want to migrate to the HDD, I'm going to -guess- that you'll have to do that "manually" (via the finder).
This isn't hard to do, just keep some notes as you go along so you don't miss anything or make "double copies".
Aside:
You -DO- want your apps and home folder on the SSD.
However, if you have LARGE libraries of music, pictures, or movies, you may want to manually locate those folder/files on the HDD...