I stripped the ram from the motherboard in my A4000 when I installed my CyberStorm mk2. (Well, except for the CHIP ram, of course!)
I did notice a slight speed increase in benchmarks vs having motherboard RAM instaled. Not more than a half percent, though. Mighta just been moon-phase or sunspots. ;-)
Certainly, though, you want to put as much RAM as you can on the CSPPC. Put the leftovers on the motherboard, if you like. If not, the absense hasn't caused me any problems...