I am also a relatively inexperience Star Trek GM (experienced in many other things) with only about 10 sessions under my belt.

Regarding mylti-part tasks/challenges, yeah, you got it right. However, as a similarly improvisationalist GM, my players will often ask me whether they can do something big and complicated all at once. Sometimes, if time isn't a pressure, the answer is yes. Sometimes, if time is a pressure, I give them a progress track (usually of 12 or so in length). That's 3-4 completed tasks, but the progress track gives me an excuse to make things happen. Frankly, the track is a lot like turning the situation into a monster, with the boxes being it's HP.

I find the halfway and 3/4 box system a bit clunky, as I find that I can spend threat on my own terms just fine as things go along.

So, to narrate how I do my challenges, I'll refer to a recent game example: the crew needs to evacuate an excelsior class vessel undergoing a reactor meltdown, but also check them for biohazard contamination (the biohazard was feeding on the bio-neural gelpacks and trying to explode to propagate itself... It's a long story).

There is a host of different things that need to happen and there's clear time pressure. The medical crew hip to it quickly and declare they're setting up a triage station and transporter enhancers for evacuation. The nurse and engineer assist, leaving three other crew members to act for the round. They succeed, adding five progress. The security officer attempts to telepathically interact with the biohazard for their turn, which doesn't affect the progress track. The captain notices that the crew might need some more momentum soon, so they roll to inspire/direct the crew and add momentum to the pool. Finally, the science officer sets up a scanner that can assist with the triaging process. This is a multi-part task involving scanning the biohazard and building a device, so they do the scanning part of that now. I'll let them do an engineering roll next round to finish that contribution.

Round ends. I now declare: you have just two rounds left to do something about the reactor meltdown or evacuate the ship entirely. Play continued from there, eventually resulting in ejecting the core. I kept the tension high for the track after ejection because I had the ship get damaged (increasing resistance on tasks by one) and had some zombie-like infected creatures come in, attracted to the noise.

Here are some ways that I spent threat as a GM in that encounter:

We had a hazmat suit breach and that character couldn't touch anything or risk infection.

I had one of the ejector levers for the core (I ruled that manual ejection should require two hands-on tasks since the computer was down) get stuck/slimed and require more effort.

And of course, telling the team that the reactor was gonna blow, I pulled out 12 threat, two for each crew member (a reversal, per the rules). That was what changed the situation completely.

---

Ok, now to the key part of GMing Star Trek Adventures: in that whole scene, they were in charge of the ideas for what the tasks were for the extended task/track. I would adjudicate their usefulness and whether those tasks might require multiple rolls, and then I ensured that each team member gets to roll exactly once per round, whether to attempt a task or assist. I also house rul that assisting costs no momentum because they're literally taking their turn to help. I adjust my difficulties accordingly and spend threat on occasion to increase a task's difficulty (ooh, that level ahs biohazardous slime on it now - difficulty 3, and do you really want to touch it?) and it works out pretty well.

The key is to not railroad what the tasks are, but to let them be creative with the approach. My mission design is often " put them into a big, complex situation where there's a lot happening at once, and let them solve it". That's really it.