I don't know for sure about the 2011 MacBook Pro, but the SATA bus is the same for both bays in my late 2008 MacBook Pro. I put the SSD in the optical bay and left the HDD in its original bay because the optical bay does not have a sudden motion sensor.
For the 2011, I'm pretty sure the internal bay is 6Gbps and the optical bay is 3Gbps so he's doing the right thing.
As for the boot, I'd say create a Mountain Lion Recovery USB recovery drive, boot from the USB drive, and then install a fresh install to the SSD. Boot to the SSD. You can migrate your Applications over using Migration Assistant if you want. Don't migrate your User directory (especially if it's too large).
Now you have a choice. You can keep your user directory on your HDD or you can move it to the SSD and then keep any large files manually on the HDD.
To keep your user directory on the HDD, activate the root account and log into it. Remove /Users from your SSD (since your user directory is empty or should be if you didn't migrate it). Now symlink the Users on your HDD to your SSD
Code:
ln -s /Volumes/<name_of_HDD>/Users /Users
You can remove everything except the Users directory on the HDD (unless there's other directories you want to keep). You won't need system directories on the HDD.
To manually keep files on your HDD, just do what you want. Or you can symlink individual directories back.