For what it's worth, here is how I proceeded when I GMed:
- If an adventure took place in a sector, I established the various distances between the various star systems that I would use during the adventures. I then used the warp speed chart (my games happened in TNG era) to find the travel times, using mostly the guidelines : 1 ly per day at warp 6, 2 ly/day at warp 7, 3 ly/day at warp 8 and 4 ly/day at warp 9.
- Otherwise, if the players had bigger distances to cross (usually that happened between two adventures), I simply ruled what the time need to go from A to B was. Any discrepancies could then be explained by varying subspace condition, cruise speed being slower or faster, and whatever technobabble I could spout should the players become really inquisitive ("then you have to stop 3 days at starbase 123 to replenish your whateverium supply").
Dunno if that helps
"The main difference between Trekkies and Manchester United fans is that Trekkies never trashed a train carriage. So why are the Trekkies the social outcasts?"
Terry Pratchett