Two seperate feed-in points for +12, -12, +5 and Gnd may very well work. I, however, would be concerned about creating "loops" in these rails. Loops can be a source of electrical noise and cause intermittant behavior. Typically, engineers and circuit board designers are strongely encouraged to provide one point source for all the power rails and avoid loops at all costs.
If the stock 1200 power connector is not enough for the MB and an accelerator (it sure should be), you could try to add copper to those main traces and connect the PS there.
A much simpler solution might be to power the HD, floppy, CDRom, etc, directly from the PS; reducing the current that must flow throught the MB and it's original connector.
