1. Mallet/spanner/extinguisher is the standard, most reliable loadout. Other options include mallet/spanner/chem (for when your pilot wants that), wrench/buff/exinguisher (or chem) (for when you want to extinguish and buff), and mallet/spanner/buff (for when you need to buff but don't need to extinguish).
2. Chem spray is an extremely useful tool that lets engineers focus on repairs/gunning rather than worrying about fire. Due to the recent changes to extinguishing (it doesn't work during cooldown anymore), you'll often be stuck with fires during hull repairs. A well-timed chem means that this isn't a problem. It's generally good to have one extinguisher and one chem spray per ship.
3. The buff hammer is so, so important to success. While the main engi should stick with mallet/spanner/fire tool, the other engineer(s) should usually have a buff hammer. It makes you more resilient, more manoeuvrable, and more powerful. A gungineer buffing their Gatling will easily outperform an enemy gungineer with an unbuffed Gatling, and that's without mentioning the buffed hull's advantage.
4. I don't really like telling people what a good general purpose ammo is, since there really isn't one (though heavy is likely your best bet). It's so gun-dependant. Always ask your captain what they want you to bring, and if they don't respond, check out the loadout and see what would go well with the guns they have.