With the Mesa Baron amp that I had that had the option of using those two tube types. I don't know if the comparison would be the same in your amp. In the Mesa the 6550's (used 6 per side), gave the amp a warmer, "rounder" perhaps more "tube-like" sound. The KT88's (both types were the winged C variety, by the way) gave the amp more punch, especially in the low-end, and sounded a bit more clean and neutral in comparison...a bit less colored in that way. YMMV, as always. My preference, by the way, were for the 6550's in that application and with my system. I tend to prefer a warmer sound in general.
Marco
Marco