I like building one space dock per unlocked fleet ship. In theory this would let me pause individual ones without reordering my queue, but mostly I don't do that. I guess each dock is like a free engineer in terms of production though, and it does mean I hit my cap a lot faster with my cheap disposable ships, the ones that I sacrifice all the time anyway, so that's useful.
Engineers are okay for repairing your ships, but in your own territory it's a lot faster to just have a mini-fortress sitting around. Unless you want to take a LOT of them with you everywhere, they're pretty slow to repair stuff on the field, and usually something with engine damage is about to die anyway so you don't always want to send engineers after it. MkIII change the math there I suppose...but if you want battlefield healing, you're probably better served with assault transports, or with a beachhead, and yeah, engineers ARE useful for beachheads.
Load a transport with one mobile constructor and like twenty engineers, and build a minifortress just on the hostile side of a wormhole. With a bunch of engineers it'll go up real fast, and now you have super fast healing on the planet, and you can start backing it up with a shield, or a huge gob of spider turrets, or anti-sniper/missile turrets. IMO that's the best use of engineers offensively. Just keep in mind that they will get chewed up by ion cannons (that doesn't mean don't use them, it just means bring more so you get the job done before they all die).