That's actually a really good question. I never looked into what differentiates the two colors but from my own experience, I tend to see solid chocolate cats has having dark-brown hues vs a brown tabby which is lighter and their stripes harder to find. As for chocolate and brown tabbies, i've noticed chocolate tabby tend to have lighter fur with darker, defined stripes while brown tabbies don't, they are more mixed and harder to spot. But that is just want I noticed. ^^
As for using them with genotypes, brown is represented by B (which is also black) because when a black cat has tabby marking, it becomes known as a brown tabby. Chocolate is represented by b.