I read somewhere that you have to make a change to allow Black Magic speed test.
As for booting, or cloning etc sometimes yes, sometimes no, and I would use CCC as it will put the recovery partition on there. And sometimes it works best to install in a drive bay or elsewhere and then just move the SSD (may not be an option with yours, you may need to install instead of use SuperDuper) why I am not sure.
Also takes longer with some PCIe boot cards and can add what seems now like a long time, 30-40 seconds longer.
Also your Mac 3,1 has 2 x 16x slots but two others are PCIe 1.1 4x and make sure the 2008 works in those slots.
I chose Sonnet Tempo and Samsung 840s after reading up on the various cards.
Real world experiences with Sonnet Tempo Pro and 2 Samsung 840 Pro SSDs
http://forums.macrumors.com/showthread.php?t=1605500
Sonnet Tempo Pro
http://www.sonnettech.com/product/tempossdpro.html
http://eshop.macsales.com/item/Sonnet%20Technologies/TSATA6SSDPR/
http://eshop.macsales.com/item/Sonnet%20Technologies/TSATA6SSDE/
Sonnet Tempo SSD Pro vs OWC Accelsior (benchmarks)
And after you clone, run Disk Utility's REPAIR DISK on the SSD -- just to be on the safest side.
http://www.macupdate.com/app/mac/37852/trim-enabler
Trim is must-have feature for most Solid State Drives. It not only increases data writing speeds, but it increases the lifetime of the SSD itself. With Trim Enabler, you can bring that feature to Mac OSX. It’s as easy as flipping a switch.
Trim Enabler can also analyze your drive and show information about it’s health and show lifetime statistics.
http://www.groths.org/trim-enabler/