I started with some guidelines I got from an old Shadis article. Basically, Technologies, (sub)Systems and Effects are put on index cards. For every "pip" in a technical skill, a player gets one card. AS GM, I gave players a choice out of a number of selections, first based on fundamentals "required" and then as the player's skill went up, he would gain the opportunity for "electives."
I based the cards on the DGP Starship Operations Manual extrapolated for TNE tech (HEPlaR and Jump Drives both gained additional subsystems, for example).
Jump Drive was a Technology card gained from Starship Engineering. It explained the basic theories, as put in the various Library data, etc. The Jump Drive System card showed the various Individual components (hull grid, fuel tankage, fuel lines, HPG, links to the Main Computer [a separate Technology/Systems card(s) that would have to be learned on their own], etc etc).
Engineers had specialty Effects they could learn. Solo Jump was the most basic (a single uncoordinated jump). Coordinated and Synchronized Jumps were other skills, as were rebuild/repair procedures. I incorporated the "alarm lights" as notifications to an individual system (which I had compiled random tables for). I would say for example to the engineer.
(As the Ship is preparing to go to jump. "You get an alarm light indicating an issue with the (random roll): power spike from the Hull Grid. He consults that card, which says how the grid gets the fuel from the line and with energy provided by the HPG, creates the jump field in the ejectected h2 "bubble" around the ship [ the paradigm for jump IMTU) and see's there's a possibility for misjump, which he can relay to the captain, who can decide if it's worth the risk or if repairs (up to and including EVA) are necessary. Done either by GM fiat, or more rolls.
If it happened while in Jump, it would be a whole lot more interesting. This, along with more random rolls, made repairs a whole lot more interesting, too. Naturally, the most skilled engineers ended up with all kinds of cards and tricks to do. Faster jump prep. Tweaked drives. Greater accuracy, less variance to the jump time, etc etc.