Collection template in the driver configuration should solve your issue.
You can use your Kobos' Serial Number to identify which collections you want to sync with which Kobo.
Something like this:
Code:
program:
if serial_number == 'put here the first Serial Number' then
add here your collections
fi;
if serial_number == 'put here the other Serial Number' then
add here your other collections
fi;
I got the idea about Template Collection + SN from a post by Chaley, so there should be some examples around on the forum.