3. Without knowing your current method or reasoning this is very hard to answer. Also if you are trying to do standard jump or squad jump makes a difference as well.
What I had been doing in my previous campaign (which I abandoned due to spending too many resources with my abortive jump station attempts) was:
1. Create fleet that I want to transfer to another system.
2. Order fleet to join jump station fleet as sub-fleet.
3. Order jump station fleet to transit.
4. Detatch sub-fleet and proceed with mission.
I was hoping to find a way to accomplish all that without needing to have my initial fleet join the jump station fleet.
Since Commercial ships always standard jump, one thing to be done is to have commercial jump tender stations at the points and then have Military ships use military jump ships.
This has been my approach in my current campaign, though I will initially be using jump drive equipped freighters to help set up mining operations in the first few star systems. I have switched to a carrier-centric fleet doctrine, and jump-drive carriers seem to be working out so far as my main jump ships. Also, I didn't realize commercial ships can't squadron jump, that may have contributed to my confusion.
On a somewhat related note, I messed up my first jump carrier design in a humorous way. I had equipped it with commercial engines for improved fuel efficiency and didn't realize that the mil-spec jump drive I equipped it with would be unable to jump the ship until it failed to transit the jump point I sent it to explore
*Edits: I can't type properly to save my life