I have two 6 week old kittens. I just switched them to stage 2 KMR but this morning I found a bloody stool. What should I do

Have they been to the vet yet? They should go get a full physical exam done by this age.

At 6 weeks old is usually when they need their first check up. Most likely the bloody stools is a result of an intestinal parasite. Sometimes they can't even test for it until 6 weeks of age due to the maturity of the worms. So I think you're doing OK. Would just definitely suggest getting that checked out asap.