o me it would make sense to have it as more of a range thing than a "you have to go there first" thing.
I mean, you really think your ship doesn't have the coordinates for DS9 stored in it's computer somewhere? That you have to buy them from Star Fleet Command before you can go there? Probably not.
Course, you're piddly little Miranda or Shi'Kar may only have enough juice to get to another location within the same sector block. A physical range on the map would be ideal (go to galaxy map, hit Transwarp, blueish circle centered on you shows which systems are within your transwarp range,and you can jump to any of them) but even if you're still restricted to just a list of systems, just increase the range as your ship gets better. So at T2 you have enough juice to jump one sector block over, so going from Memory Alpha to K7 would be a jump to Sol, then a jump to K7. Then at T3 you could jump the whole distance in one go, as they have the power to transition 2 sector blocks.
Personally, I'd want to be able to jump to any system within a range bubble based on ship, myself.
i think that a lot of the transwarp conduits are static (based on a few missions out of Starbase 39 Sierra) and so what you are really doing is tapping into an existing nearby conduit and going to one of the predetermined destinations (one end or the other). If you don't have the info about the dynamics of the conduit, then you have to go to one of the ends to enter the portal in order to enter it. so each sector block should have a set of conduits that connect it to sirrus and possibly others.
also like in the missions, these conduits could (in neutral zone etc) become contested areas and have to be protected from capture. in order to protect the areas connected via the conduits from unexpected invasion.