sata III and p5k

The board should support booting from a card but you need to make sure the card supports booting from itself (not all cards do).
 
From what I can tell from the manual (assuming I'm reading the right one) is that the blue PCIe 16x slot always runs at 16x. The black slot, despite being 16x sized, only runs up to 4x speed because of the limited number of lanes available from the P35 chipset.

What I will suggest is that you avoid PCIe 1x cards, the P35 chipset is only PCIe rev 1.1 so a 1x card is limited to 250Mb/s so will bottleneck a decent SATA3 SSD.
 
Not sure what the Asus U3S6 runs at. Says compatible with 16x but that doesn't tell me anything.
 
Usually when you install an add in board you'll get an option in the Hard Drive boot order section of your BIOS that will point to the controller card. Then you use the controller cards BIOS to set the individual boot order of devices connected to it.
 
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