Is the Kingdom of Jade supposed to be east or west of theTransitive Isles?
What about the other Far Lands? Where are they? Avenroc is supposed to be off to the Southwest somewhere, and Valhyr is supposed to be to the north. What about The Imperium and Ea?
Relative geography in the Transitive Isles has always been deliberately vague.
The meta-game goal was to create a world where different DMs could have the freedom to interpret the world as they see fit without stepping on each other's toes. Thus, if in one game the PCs travel east by boat to get to the KoJ, and in the next game they travel south on foot and get to the same place, there's no contradiction; both DMs are right. If a third DM comes along and has his players get there by going straight up in a hot air balloon, well, they're right too. The world isn't linearly connected in the same way that ours is; the connections between one place and another are transient and unreliable. Thus, there effectively can't be a single World Map describing where everything is in relation to each other. If you walked into a bar in Daunton and asked in-character for someone to point in the direction of the KoJ, they'd all just look at you funny. Much the same kind of looks you'd get if you walked into an American sports bar and asked what kind of components to use in a Raise Dead ritual.
That much is relatively canon; what follows is me musing on how that might work in daily life.
How do people reliably get from one place to another, then? Well, first of all, the transitive effect is stronger on a larger scale. If you have line of sight to your destination, it's probably going to hold still for long enough for you to get there. For longer trips, I imagine that the inhabitants of the world have, to a greater or lesser degree, an instinctive intuition on how to get to places. If you are going from the Hanged Man to the Temple of Lauto, you'll know that you need to go three blocks north, hang a right, cross the bridge, and go straight until you can see the spire -- even if when you made the same trip yesterday, the Temple was on this side of the bridge and to the south of the Hanged Man. It's just instinct, as unremarkable and prosaic as gravity.
I imagine that some people have a greater innate talent for finding places than others. Those people tend to find work as explorers, guides, caravan masters, navigators for ships, etc. A good navigator can shorten your journey considerably, while a bad one, or just an average person, will usually get to their destination eventually, but the journey may take many times longer and lead through dangerous diversions.
Consider a trip from Daunton to the Kingdom of Jade. The best possible way to get there is by using a portal ritual, sidestepping all this travel nonsense. Failing that, if you have a good navigator who's been there before, you do what they tell you and you'll probably have a fairly uneventful journey of a week or two, but the navigator will expect to be well paid. Pissing off your navigator is Not A Good Idea. If you have a good navigator who has never been there, the journey will probably be longer, perhaps a month or two, and involve some detours, possibly moderately dangerous ones. If you set out without a navigator, or with a bad one, you'd be lucky to make it there alive, and if you did it could take six months or more. Of course, all of this is variable; sometimes the conditions for travel are better or worse, subject to the whims of the DM.
Mechanically, a DM could model this navigation as a skill challenge, using things like Nature (or Dungeoneering, if underground), Perception, Insight, etc. We've all seen skill challenges like that before. Or, you could use an NPC guide who "knows" where they're going. Or, you could just describe whatever geographic relationship you feel like, and that's what the PCs instinctively know about that journey. Thus, "The island nation of Hoboken lies three days' sail off the far coast of Daunton," is not so much a declaration of a permanent fact about the world, as a summary of the speaker's current intuition about how best to get there.
Would it help cleanse my burden if I said it was only because I liked the Wing Commander games so much? 
