As an engineer I go for Mallet/spanner/extinguisher (since I've played so little) because I usually do not know if the other engineer has the capability to put out fires. If the other one has the same loadout, no problem because that combo works for two engineers. If the other engineer has something akin to a spanner/buff/mallet or freakish buff/mallet/extinguisher I can still keep most of the ship running.
What I do is ask the other engi, or engis what there load out is before hand. This way I can set my load out to balance or compensate for what the other lacks. Though as a good rule of thumb a basic and idea load out for a new, or even experienced player is mallet/spanner/chem spray OR extinguisher. However, a decent load out with a little practice that I would recommend for gungineers particularly is wrench/buff hammer/chem spray. This combination works well as general use, have managed it and even preferred it on certain ships like the squid. Mostly though it is important to communicate with your teammates and captain as to what is necessary to bring and do. Just my two-cents.