Hmmmmmmm.....
According to the RSim file on EMRR - modifying it by removing the 18mm engine tube and block from the booster and making it a 24mm booster - you have to double the nose weight to maintain stability in the 2 stage configuration. This greatly offsets the OOMPH delivered by the larger D booster, and only about 150 ft in altitude gain is realized (I'm suprised by this....)
Anyway, with that said, If all that is gained is 150 ft I'd stick with the 2 x 18mm configuration in the kit. That way, you don't have to add additional nose weight and you'll have a better performing rocket if flown as a single stage rocket without the booster. Plus, C's are cheaper than D's.
Have fun!