I never actually understood how this works. But from my experience, in order to set up 2 different weapon groups, i have to actually cycle through 3 weapon groups to get to my next setting otherwise it doesnt work.

Example:

Ship-Valk

What I would like:
-Group 1:
Primary fire- 2 neuts
Secondary fire- flare

-Group 2: Primary fire- 1 neut
Secondary fire- 1 neut
Tertiary fire- flare

What I have to do:
After setting up the weapons in their groups, I press 2,3,4 in order to go from group 1 to group 2. Then to switch back I have to press 3,2,1. If I don't cycle in this order my weapon groups get all screwed up.

Is there an easier way to do this? It's quite possible I've just been setting it up wrong for a year and a half...

Use binds? (Don't remember how, check the thread about custom binds)

Each of the lines in the pretty list you see when choosing weapon groups has its own little command, called weapon#, where the # is the number of the line. So, weapon1 causes you to select the first primary fire option, weapon2 selects the second, and weapon3 selects the first secondary option[See the edit at le bottom]. You can mix and match these as your heart desires, which is part of the point of assigning a different key to each one, and probably why they're not labeled in a recurring pattern of ones and twos, but are rather numbered one through seven.

Now, what you're wanting is easy enough with a simple bind along the lines of

alias LOLZGROUPONE "weapon1 ; missile3 ; mine6; alias LOLZSWITCH LOLZGROUPTWO"
alias LOLZGROUPTWO "weapon2 ; missile4 ; mine7; alias LOLZSWITCH LOLZGROUPONE"
alias LOLZSWITCH LOLZGROUPONE

With that three-liner, you can bind LOLZSWITCH to whatever button looks sexiest to you at the moment, and bam! An instant weapon group switcher for whole groups of weapons! AMAZING! Hell, you could even throw in an echo or two, to make sure you can tell what you're switching to!

Edit: The furry brought up an excellent point which I've overlooked, the commands for secondary and tetrariry fire actually start with missile and mine, respectivly. Editing lolerbind to reflect DA TRUTH.

Man it looks nice, but I can't quite figure out how to get the goo off (that's hair conditioner.... right? Oh god please tell me its conditioner...)

In the example you cite, I would set up the weapon groups so that primary fire is either 1 neut or 2 neuts (toggle with 1/2), secondary fire is always 1x neut, tertiary fire is always flare.

That way you cycle between the option of auto 2x neut+flare or manual chainfire neutx2+flare just by pressing 1 or 2, which I think is the effect you're looking for here.

Straight from my wgaf.cfg (and more intuitive than the troll's bullshit)

alias wepswitch "wepswitch1"
alias wepswitch1 "Weapon1; Missile1; alias wepswitch wepswitch2; echo '[][][] Primary Weapon Mode Activated [][][]'"
alias wepswitch2 "Weapon2; Missile2; alias wepswitch wepswitch1; echo '[][][] Assault Weapon Mode Activated [][][]'"
bind "X" wepswitch

It toggles between the first and second selections for primary and secondary fire when activated.

I use it essentially the same way you mentioned, Ghost, only I like to fly one energy weap and two flares. I set energy to group 1 primary and dual rockets to the first secondary group. (Primary weapon mode) and I set one rocket to the second primary group and the other to the second secondary group for Assault weapon mode. Whatever you set as tertiary remains tertiary, so if you have a tertiary missile (like in the case of my rag) you'll still have it, but if you don't, you can set your first primary (disabled by the bind) to be available on tertiary.