Generally a pilot is two things: helmsman (obviously) and commander. Commanding is the harder but more important skill to master, and I find there are a few important aspects:
Voice communication: use of a microphone is critical, since typed commands will go unnoticed until they're too late to be helpful, and typing means you're not piloting or doing whatever else you need to be doing.
Situational Awareness: in a fight, gunners will usually only notice what they're aiming at (even between reloads), and typical engineers will be too busy looking at the inside of your ship to notice what's going on with the outside. Make sure you don't focus your attention solely on a single enemy ship: as both a pilot and a commander, you need to be visually skimming your entire field of view periodically, calling out enemies, and notifying your crew about terrain that you can't avoid or lag spikes you're experiencing, if and when it occurs (it can be helpful for gun crews to distinguish between a captain turning to acquire a new target, or spinning due to loss of control). Be sure to keep a constant eye on the status of your components. Applying this sense correctly, it's not uncommon to be able to manage simultaneous, sustained attacks on two or more enemies.
Exert a sense of control: your crew should sense that you have a plan (even if you don't actually have one). By plan, I mean some short-term goal you're trying to achieve (or continue achieving) over the next several seconds. Based on your active situational awareness and that plan, you know which components need to be prioritized and which will not. There may be times when you need engines but don't care about a balloon, or your team is leading by 3 kills, but the enemy will soon regroup and you need everyone on guns more than you need them repairing your hull. Unless the crew can read your mind, they can't situationally prioritize, and so you do need to tell them what to focus on.
I regularly inform my crew when I'm about to use a skill that damages engines (it allows engineers to get in position, and keeps the crew from thinking you're under fire when you're not), or when I'm going to ram, and particularly which fields of fire I expect to open up. You'll also find gunners keep trying to track an enemy that you're turning away from, until you tell them to aim toward another enemy (when switching targets, it helps if you can tell them where to aim, relative to their current viewpoint).
Invite the crew to make suggestions: since you're not the one gunning, take requests for loadout changes. Certainly a lumberjack will be less useful in the canyons than it will be on the dunes, and your ship and configuration should reflect the map and complement friendlies while countering enemies, there will usually be several applicable weapon/ship combinations that play well into your style, so it can help in those cases to determine crew preference. Discussing it is best left for private crew chat, rather than lobby voice chat, of course. Good engineers and gunners will direct your attention to things you may not be noticing -- that's a good thing!
Coordinate with your team: particularly with new allied captains, you'll be trying to manage the team dynamic quite a bit too: it hurts your team quite a bit if one of your ships keeps dashing off into 1v3 battles, or is sight-seeing in capture point matches. Even with competent allies, great coordination can allow a pair mediocre crews to isolate and defeat strong opponents.
Use pilot abilities: in fact, it can help to have 3 abilities rather than 2 and a spyglass. Your crew will generally each have a spyglass (were they planning on piloting your ship?), and should be spotting ships for you (feel free to tell them to spot ships, and remind them that without the targeting reticule, you won't be able to line your ship up in the thick of three-dimensional battle for good shots anyway). If you're not regularly employing your abilities, you'll be at a definite disadvantage.
