So, here are some brain examples files. In the folder "data/missions/warriors" you can find more examples, these here are neutral shells.
Note the FSM ID at the beginning. it must be unique, you cannot have two brainfiles with the same ID inside your MCO installation. The files are easily edited in a text editor. Techically, it's just a matter of inserting the correct mission goal numbers, Squad Id's and X,Y Positions and maybe some ranges. Also note, that the goal numbers from the editor start counting with "0", not 1 (First goal is goal number 0)
To assign the brains, just insert the file name into the mission.fit file in your missions folder (when you create a mission called "test", then there will be a "test.fit" file. Search the Squad ID and replace the filenames, without the .abl extension.
http://omnitech.hard-light.net/team/starman/downloads/Brain_examples.rarIf you wish, I can give you my guide for "advanced mission programming". Currently, it's still WIP, and I forgot the newest version on my company laptop, which I cannot access the next 2 weeks. So the version I have here is lacking 2 chapters. But it's quite complicated for non-coders.
As for your campaign problem :
Open campaign editor, there you see the groups in the box , klick edit group, then you see the missions inside the group. Click on edit mission. There you can control wether logistic shall come up for each mission or not.
Note, the first campaign mission always starts without logistics.
Hope that helps.
Your catapults most certainly only perform a guard command. Give them a powerup move command.
Note sure what you mean with neutral mechs. You cannot change the mech descriptions ingame so easily. If you want to have a mech a special name, you have to give him a seperate variant in the mech object file.