I'd probably just hook the SSD up to the mobo so you can avoid any boot issues (and possible bandwidth restrictions from the add-on card sharing 1 lane across up to 4 storage devices transferring data at a time). Plug your secondary storage drive into the add-on card.
I can't find anything that matches exactly what you're asking (not to say it doesn't exist). I did find this unit with 2 external USB and 2 Internal SATA
though. You could always do it old-school (aka early USB3.0 days) where you run a cable from the rear panel back into the case. This card has an internal USB3.0 header
and you could run a USB3.0 to eSATA cable back into your case from the rear panel. Here's a link to adapters to fit each scenario.
Main: i5-3570K, ASRock Z77 Pro4-M, Asus GTX660 TOP, 500GB Crucial BX100, 2 TB Samsung EcoGreen F4, 16GB 1600MHz G.Skill @1.25V, EVGA 550-G2, Silverstone PS07B
HTPC: A8-5600K, MSI FM2-A75IA-E53, 4TB Seagate SSHD, 8GB 1866MHz G.Skill, Crosley D-25 Case Mod