I looked at all the advice in the FAQ, but it's not really helping -- I'm at the point in the game where you face an unavoidable fight with one of the brothers (at least, I think it's unavoidable -- it seemed to be implied that even if I killed both remaining pangolins an executioner would be gunning for me anyway) and I just plain don't know what the hell I'm doing.

I'll fill my body with red, blue, and green, and have more or less halfway full portions of each color in my palette, but I just can't do enough damage to any of the brothers to make a difference. I've tried to fight two so far: the one made of wheels and cannons whose face can move from his top tube to his torso, and the guy with a sword for a head who has his face on his back.

With both brothers, I have hte same problem: I can do a little damage by painting color onto their hidden face, but nowhere near enough to kill them. It seems as if I would have to fill every single color in my palette to the brim to have enough ammo to take one of these guys down, and even then I'd effectively be out of color (and besides which, it's too late for me to just sit around and transfer color to my palette while waiting for the fight).

Is there something I'm doing wrong here?

Aside from one brother, whacking them with gobs of colour is not particularly effective. If possible, try to get some of the attack glyphs like Hawk, Owl and in particular Ritual before engaing a brother.

During my first playthrough I was getting friendly with Ava which somehow annoyed Whaler (swordhead) immensly. I tried pelting him with colour and found that it was barely doing anything, then I put down the three Ritual glyphs (32 colour each) and then BOOM, half his health had gone.

I have noticed that certain brothers are more susceptable to certain glyphs - using the above example, another brother was devestated by Ritual but Ironclad and Mantid took barely a scratch. Aside from this, watch the wheel rotating in the top right corner and hit the brother with the corresponding colour. Be sure to have plenty of red in your hearts as it will do more damage.

Is there a list of those weaknesses anywhere, or something? Because none of the glyphs I've tried seem to work on, uh, anyone. All the projectile ones do as much damage as just lobbing color at them, the guys I'm fighting evidently aren't susceptible to ritual, and the S-shaped one does next to nothing.

My favorites are ritual and hawk.
Ritual needs a total of 90 drops of colour but completely nukes the enemy and hawk does moderate damage and can be redirected in case you miss the enemy. You can also try owl on cage guy and Montgolfiere and I think drill guy is weak against it too. Whaler and the wheelchair-man usually come towards you in a straight line so wasp works pretty well.

By the way the boss weakness list is a pretty good idea hold on a second.

I'm afraid there are few weaknesses, actually... The system is much easier than it seems: most glyphs do one and the same damage per drop of colour, and what differs is how suitable its way of work is to take down particular enemy. Though, exploding boulders do a bit more damage, than all these usual variations of tumbleweed with lympha inside:).
My favorites for the beginning of the game are Wasp and Sleeper, as they usually pop near the beginning, and may be used against almost all enemies. Owl or Tumbleweed are a good choice for the fight with Warden (and Juggler too). It's hard to take him down with Wasp (because he moves constantly).
Some tricks
- S-shaped glyph seems to deal a good damage at a certain distance, i.e. it consists of a number of "damaging points" that move away from the player. If your get many of the point hitting the target, the damage may be huge. However, they don't do much harm NEAR you.
- when you use Magnet, you can punch the "gravity ball" so that it hits the enemy. If the objects collected by magnet do harm, the brother will be damaged.
- Whaler becomes stronger and faster with each head he gets, but his defense becomes weaker at the same time. The fight is lost if he has 4 head, but 3 heads will let you defeat him with the least lympha expenditure.
- Ironclad has just the most hitpoints. That's why he is tough to kill. Ritual is quite effective to deal with all his small portable cannons at once. Magnet can also serve this purpose: just collect all the cannons in one corner of the level, and don't go anywhere near.
- Patriarch is not only quite an average Brother, characteristics-wise, but has an additional way to kill him with even more ease. The boulders lying all around the level can be set on him. First paint over the boulder with a drop of colour, and then use a drop of colour on the Patriarch.
- use Shell with Triumphator.
- Pit's drills can hardly ever reach you if you quickly get to the opposite side of the arena after the brother springs out the ground. Note also that each time he tries to appear as close to your position as possible.

Actually, I seem to have solved the problem just by utilizing the rotating color wheel on the boss's HUD -- a friend told me what it was for, and I took down Warden with four or five owls in a relatively short period of time. I feel like a moron for not assuming those rotating colors corresponded to weaknesses (though I am colorblind, so I'll use that as an excuse whenever possible).

It's written in the manual
Though, nowhere else (not even in the game).

Got it from Steam -- couldn't find the manual anywhere.

It should be in the folder with the game.

Steam version's got the manual, it's found in the directory: steam\steamapps\common\The Void