Thank you for sharing more detail.
I would check the motherboard to see if the chipset already supports a HBA. In the fully built system the HL-15 is using the 2 motherboard chips to manage the drives (from a previous post):
the backplane had 4 sets or 4 drives connected with 1 Molex and 1 HBA cable for data. the reason we switched to this design was for the performance. our older designs where it had a multiplexer on the backplane which allowed 5 drives to connect to 1 HBA cable.
When it comes to JBOD for your needs, it really depends on what file system you will use.
For myself, I ruled out JBOD because I wanted to use a storage format that would provide redundancy. The redundancy would allow me to remove/replace a drive, etc.