- always have lots of engineering spaces (I usually put in three)?
That's the problem. 3 engineering spaces is absolutely NOT enough, unless the ship is very small. Your ships will break all the time and use a ton of supplies.
You cannot simply choose a number and use that, it heavily depends on how big the ship is. Engineering spaces both add maintenance supplies AND make component failures less common, thus saving maintenance supplies.
I add engineering sections until I hit about 2 years maintenance life at the LEAST for ANY kind of military ship. No exceptions but fighters and FACS. Civilian ships instead need just one no matter their size to last forever.
After that it heavily depends on the type of ship.
- Ships intended for system defense: After task force training to 100%, these will generally stay in orbit around a maintenance facilities equipped world. As such, 2 years is enough because the maintenance clock will not increase, so no maintenance supply consumption.
- Mobile/offensive fleets: minimum 2 years as above, but if the deployment time is longer, maintenance life MUST be a bit higher than deployment time. If deployment time is 3 years, for example, I add engineering spaces until it is 3 years and half or something. These fleets will be expected to spend some time away from home regularly, they must be capable of doing so without breaking down all the time. If they are not being used at the moment (no enemy, no hot spots, no interceprion), these too get parked in orbit around a maintenance facilities equipped colony after TF training to 100%. Use the lulls between fights to overhaul them, but NEVER do so if you fear a strong attack, and never of the whole fleet at once. I try to never have more than 33% of my fleets in overhaul.
- Gate guard/other immobile ships away from colonies: if the design allows it, I go for at least 5 years maintenance life. Overhaul once the maintenance counter comes close to maintenance life, in the above example I'd overhaul every 4 years or so.
Please note there are other bonuses to having more engineering spaces: the ships will repair faster after combat if there is ship damage, AND you can repair more/bigger components. That's the difference between a damaged ship marooned in enemy territory and one who can repair the engine and get back home.
You will use a lot of minerals for overhaul anyway,but that is the price for having a fleet. But no industrial capacity will be needed (except in rare cases), and your ships will last longer.
P.S for long time operations you will eventually add dedicated ships o your fleets, like tankers for fuel, colliers for spare missiles and supply ships to carry maintenance supplies. These ships will be left behind generally during the heat of combat, and rejoin the main fleet in the pauses to refuel/resupply/rearm your combat ships.