Oh jeeze. SATA port multipliers are hugely problematic because very few controllers actually support it since it's not part of the specification. This includes the Intel ICH/PCH controllers and most add in cards. If you want to go with the single initiator -> multiple target approach you're best off using an SAS controller which should support SATA port splitting by design.
The chances of that tower working with anything that you have are extremely slim. Get a proper RAID enclosure which exposes a single disk
This is the RAID card I have, but it doesn't work in the PCIe 3.0 slot on my mobo. (It works in the PCIe x1 slot, but that's covered by my gpu)
My understanding was that I could use that card with that tower for port multiplication.
Do you have any recommendations on a different RAID card? It needs to work with that tower, work in a PCIe 3.0 slot, have at least one eSATA port, support RAID 0/1/5/10 in Win7 and Linux, and be a low profile card (so not to interfere with my GPU cooling)
I'll look into SAS, but I'd rather eSATA since I already have a tower for it.