Most of what Gregmac has said is correct, however I have to correct a couple of small items. It is totally acceptable and often done to use a three wire circuit (black/red hot, white neutral & bare ground) like you have to "alternate" kitchen receptacles, thus giving you two circuits. It is not a code requirement to split the top and bottom of the recpts, however it is fine to do that, but it complicates the GFI functions. Splitting the top and bottom would require two GFI's upstream, one feeding each of the legs. More common would be two single pole GFI breakers in the panel.
With that said, your situation is different. I bet you will find that the the black feeds every other recpt, and likewise the red does the same thing with alternate recpts. Once you confirm that, simply install a GFI on the first powered recpt of each string (color). As a matter of fact, this is the most common way kitchens are wired and meets NEC.
