The way I do it is I just decide what I want to dedicate the pipe to - latakia, burley, VAs, aromatics, etc. I generally dedicate smaller bowls for VA flakes, but that's a pretty loose generalization. I don't have any strict rules about it.
I might sometimes find that a certain pipe is a little off with certain blends, and I have on occasion changed a pipe from one type to another and found it works better. This would be the trial and error part. But it only takes place after a more or less arbitrary decision.