Only way I've got external SSD's working is with setting up the original PCIe disk and using winclone on iMac's and MBP using thunderbolt enclosures hosting them. Not got one going in a Mac Pro tower cos PCIe SATA cards have to have a bios to boot windows properly in legacy mode and I don't think many SATA cards bios support the ESATA port for booting windows.
I've had to use twin SSD's off a solo x2 SATA 3 PCIe card in my 3,1 to boot windows properly. Having the windows partition on the same SSD it just wouldn't boot off it full stop which Apricorn say is a 3,1 specific problem. I had to use sticky thermal pads to stick a second 840 evo on top of the other which screws in the card, use the x2's second SATA port to connect and use power off the optical power extension I've run for the usb PCIe 3.0 card. Now I have SATA 3 on both OSX and windows 7. I installed windows and bootcamp in sled 2, ran the x2 empty to let windows install the driver, patched the mbr, got intel AHCI going with MSAHCI then upgraded to the 10.1.1008 rst driver only. That's the latest rst for my 3,1 and does not have the 3tb drive bug. Then I moved the 840 evo from sled 2, stuck it on top of the first SSD and finally it works great, leaving my sleds free for spinning disks.
It was probably the biggest pita bootcamp I've done but was cos I wanted SATA 3 or bust for dual booting windows and OSX. Though it takes a little longer to boot I do notice it's quite a bit faster in all round use, get about 470mb instead of 270 in a sled.