Balancing missions is one of the harder aspects of the ALiVE mod, because a lot of how you go about doing it is going to depend on a lot of factors (number of humans, how much involvement you want from friendly AI, long term persistent campaign or one-off mission, AO size, how much interference you want from friendly groups or if you want to do most the fighting yourself and call in groups afterwards, etc).

I think the best thing you can do is go with your gut. Then before actually "playing," fast-forwarding the mission in the SP editor for a few hours with virtual AI and maybe even OPCOM debugged, and watching how things play out, and then making your final tweaks from there.

I have missions ranging from stuff with a set objective designed to be completed in one sitting (with no friendly AI interference at all. Kind of like a special forces thing), to full map long-term persistent insurgencies, where having at least some friendly AI available, to help you out if you need it, is pretty much critical.

You just need to decide what kind of op it is, and what you want out of the experience. There is really no set way; just means (the mod) and resources (such as the forums here) to achieve your goal.