Best way to expand JBOD with RAID?
First of you you cannot expand a RAID-1 (Mirror). If you want to make a larger RAID array you will have to back up the drives and recreate the RAID array in a different configuration.

Once you have done that you have several configuration options with 4 disks. A quick google of types of RAID will show that... However if it were me I would set up the 4 3TB drives as a RAID-5. Yielding 9TB of disk space. That makes all disks in the enclosure part of the same array. 

There is a problem with that though. Disk Utility will only give you RAID-0 or RAID-1 (non-redundant stripe or mirror). Which means that you would have to purchase a third party RAID utility to do RAID-5. There are a couple out there and I have heard they do a good job. Depending on your budget that would work well.

Your other (no cost) option is to put the other two disks in your enclosure and just set them up as a second RAID-1 array. It won't give you the speed or as much space as a RAID-5 (6TB total usable space) but it will work just fine and show up on your Mac as a second volume.