Hi Paul,
There's no right or wrong way to do it, but something I've done in the past for stages that don't have a traditional 'upstage' and 'downstage' is to assign each wall of the theater a direction - 'north south east and west'. That way you can note that an actor crosses north, or exits southwest. You can also use positions on a clock, or assign specific walls to be upstage and downstage (though that can be unhelpful, if you're trying to play to both sides of the house, if you think of one of them as 'downstage'.
Whatever method you choose, it's useful to put a note in the rehearsal report at the beginning of the process to let other people know which wall you're referring to as 'north'.
EDIT: And it's important to put signs on the wall in the rehearsal room, so that actors know which way to go when the director says "Exit through the South door" or something similar.