Canon Pixima Pro9000 mk2 -- how do I transition to refill ink

I will be starting to use a new Pro9000 mk2 soon. It has 8 Cannon ink cartridges that came with the printer. As they run out, I want to transition to ink refills from independent suppliers-- either a Refillable cartridge kit #9 from Media Street, ink from Precision Colors, or OCP ink.

I'm not a photo-pro -- but I have read this forum extensively and understand that different inks should use a different color profile (paper too). Question is: when the first ink cartridge needs replacing (or refilling), what do I do?...that is do I replace just that one with the substitute ink (seems like this would screw up the color profile), or do I have to waste all the remaining ink, and replace all the cartridges?

Any other tips, suggestions for the best combination of ink quality, cost, and refill ease would be appreciated. This forum has already saved me a bundle by pointing out the Craigslist opportunity to buy this printer -- I got mine for $175.