Lightroom mobile syncs to only one catalog. Did you start Lightroom mobile before setting up a desktop catalog?
You can use Import from another Catalog in the file menu to get the files into the main catalog (do it from the main catalog, selecting the small catalog on the SSD).
You'll need to sync Lightroom mobile to the main catalog then.
Sorry.. I just realized that I was probably using the wrong terminology. Here's a bit more detail:
I upgraded from Lightroom 4 to Lightroom CC. My catalog was updated to this new version and is called Lightroom.lrcat. I then installed Lightroom Mobile on my iPhone and synced it to my iMac.
Now on my iMac's Lightroom, I see a folder called "From Lr mobile" which contains all the pictures from my iPhone that have been synced over to the desktop. When I choose to "Show in Finder", it points to a Mobile Downloads.lrdata file which acts as a package that contains all the pictures from my iPhone but resides on my iMac's small SSD drive. I was hoping to have all my iPhone / iPad pictures be added to my Thunderbolt mirrored drive instead as it has a lot more room (and is automatically duplicated since it is a RAID configuration).
Ah.. that makes more sense.
You could just move the files into a different folder in Lightroom (on your main drive) and add them to a different sync collection. Of course new files will go to the From Lr mobile location.
I am not sure I can explain this in proper detail, but maybe this will help.
I went into Catalog settings way back when I first started using Lightroom. I told it to set up the catalog on one of my spinning drives as to not fill up my SSD. So it sits in G:/Pictures/Lightroom.
Inside that directory is one called "Mobile Downloads.lrdata". Digging into that reveals the images I am sharing from my phone.
My guess is that it has to reside on the same drive as the catalog. Is your catalog on the same drive as your images?
There is an Idea on the Feedback site requesting what you are asking.
Please go to " Lightroom: Allow Mobile Downloads.lrdata to be moved to another location " and vote for it. More votes = more chances to have it done.