Portal

Works like this as example:

You need to build 2 Portals as system Improvement on your owned star Systems (or Optional 1 Portal and use the one of an allied Pirate Base). After you build the Portal(s) your fleets will automatically use the portals on their pathfinding if it will shorten their way to their destination. Meaning that if you got 2 Portals build up and ready on 2 Star Systems and they would be both on the opposides of the galaxie, they will use the portals of the star system they are orbiting OR nearby star system and directly teleport to the other Portal closest to your fleets destination.

Alternately if you got 1 Portal build at your Star Systems improvements and a fleet at/nearby the star system and there is an allied Pirate Base nearbly at your fleets destination, they will teleport to your allys Pirate Base and head to your fleets destination from there (in case its closer to the destination then your own Portals)

Of course you need to watch having the right technologys unlocked at your research tree to be able to do this respectively

Hope i could help your with this

I usually build portal in every systems, then transport minor faction population between systems.