How do you know where to start numbering with chair conformations?

Anywhere. It's just the 3d conformation that the benzene ring has. When you start numbering benzene rings you generally start with the carbon at the top but since the chair conformation doesn't have a ';top'; per se you just number from wherever. If it has a functional group, you start with the carbon attached to the functional group just as in the flat structure of a benzene ring.