I have never tried to run two psu's connected to the same board. I have hotswapped ATX12v, AUX, and 4 pin Molex's before, in a variety of boards, it never resulted in dead hardware.
I could see a possible problem if you turned on your secondary psu before your main psu, it could cause problems with the rest of the 12v items on your board.
If you aren't suffering with any stability issues then I just wouldn't bother with what you are suggesting, there is just too much chance to blow something up.
Even if your system was unstable, I'd just buy a single large power supply, and be done with it
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2x P3 1100's at 1400, Abit VP6, 2x Corsair 256mb PC150 sticks, 20gb 'cuda ATA-III, 2x 40gb 'cuda ATA-IV in raid 0. 20" Trinitron. No fans
2x 2400+ at 2288mhz (16.0 x 143), Iwill MPX2, 2x Kingmax PC-3200 256mb sticks, 4x 20gb 60gxp in Raid 5 on a Promise SX6000. Asus Ti4200 320/630. Cooled by Water
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