I had left my CJ 500 with it set as pigment just because it was there already. Not sure if it would matter if you make your own profile as it would adjust the inks to get the right color.
One thing that may make more of a difference is selcting just CMYK and not CMYKLcLm in the rip.
It may want to do a change of ink if you select to change the ink set. If it does and you can't get out of it, just pause the printer or turn off and remove the pump lines from the captops and let it do its thing and then you won't waste ink on a pump out. These printers just pump for a time period and then stop thinking its done.