Mostly it comes down to some pretty specific personal preferences, but I'll try to lay those out (this is not necessarily an optimal method for everyone - that's what I like about AI War, everyone can play it differently!)
Mk1 fighters take 2 seconds to build, mk2 take 4 seconds to build
Mk1 missile frigates take what is it, 14 seconds to build and 28 seconds for mk2?
And the bonus ship, it varies.
I place extremely high value on having fighters available at all times because of them being so versatile. Also, because frigates are so expensive and take so long to build, sticking them in the same build queue with my fighters will make it so that it takes forever to rebuild any fighter losses I've incurred. This is why I separate my production of ship classes between different factories rather than mixing ship type building (though I will assign different marks of the same ship to the same factory)
I don't assign engineers to assist because of a couple of reasons:
-engineers are expensive, and the thing that crashes my economy fastest early-game is when the 5 auto-build engineers and rebuilders start building from the controls tab.
-It's not uncommon that even with the additional forcefield protections, that factories end up getting blown up. Having 7 (or 9 if it's after I've taken a couple planets and I've added two factories for bomber production, add 2 more for every additional ship unlocked) factories instead of 3 means that if I do lose factories I can shift production non-critical production to fighters (or my bonus ship(s), whichever is more useful at present). There have been a couple games I've lost because I forgot to build counter-sniper turrets near my home command station, and then snipers blew up all my factories and I wasn't able to reinforce during the battle.
-Mk2 engineers have very low utility for me, and the knowledge is otherwise worth a lot to me, so I try to economize on my engineers by keeping them available for emergencies. Because my empire is not necessarily contiguous (and even if it is, there's too much AIP cost in trying to choke-point my entrance through any method other than gate-raiding), I tend to maintain 5 mk1 engineers on my most at-risk planets.
-Ease of resource accounting: I know exactly how much I'll be paying per second per factory if I don't use engineers, and when I'll be getting each ship. I could probably do the math for engineers (the build times change when you assign engineers, so that's not difficult), but it would be something I'd have to keep re-referencing, and I want my production to just go without a hitch and without having to monitor it. I also don't want to deal with having to micro my engineers every time they get destroyed by some rogue raid starship.
If my engineers haven't been told not to auto-assist, I have no clue quite what's being built when or where resources are going without constantly watching them. I never let my engineers auto-assist my factories.
This is general. If it's a multi-homeworld start where resources are less of an issue, my build changes.
