can i use migration assistant to migrate files to a secondary drive?
Not easily can you let migration assistant handle that task. Instead I would migrate everything but the user accounts to the new drive. Then do some reading on options and mechanics:


http://mattgemmell.com/using-os-x-with-an-ssd-plus-hdd-setup/
Optimize macbook pro for internal SSD+HDD drives
One mac, Two or more storage devices - how to divide things?


My guess is putting the user folders on the second drive is the easiest for you and best result. Start by making one admin account with the same short name as your preferred main account on the old Mac. 

It will make /Users/whatever on the boot drive. Then you can copy all of users from the migration donor Mac to the large new drive. Use rsync or something that can run several passes or resume a broken transfer if you can, or be patient with finder if you can’t. 

At the end, you’ll use advanced settings in the user preference pane to point the home folder(s) for each account needed to the second drive home folder.