Create a SATNUM array, with different integer values for each of the facies you believe has a different rel perm curve. If you define (for example) SATNUM valules of 1-5 in your model, you then need to specify 5 sets of rel perm tables

Regarding shales, just assign them as one of your poorer facies - it will be pretty well irrelevant anyway as their perm should be very low, and their overall saturation is unlikely to change from the initial saturation to any significant degree - you may want to seriously consider assigning their NTG = 0 or PORO = 0 anyway to speed up simulation unless of course vertical flow across the shales is important in your model