I have gone over this a bit in the updates, but I'll lay it out a bit better for you here.
Currently, your corporation focuses on producing
civilian-level biotech augmentations. It also produces
basic cyber security systems, which isn't something I've outlined in the updates so far. Beyond that, several businesses "donate" you portions of their weekly earnings, thanks to the blackmail materials you stole from the Syndicate. The $1-1.5m a month is projected earnings from those.
Your security budget represents an enormous portion of the budget the company has. This is because Alfonso believes that you are going to use those funds to provide him with assets he can use to generate more funds than he puts into your budget. So far, you haven't, but at the same time, so far, you've mostly been spending the personal assets Ezmerelda donated to her security budget. Of the money Alfonso has allocated you, you've only spent
$2m. You've definitely made the business back some of that. Ezmerelda has lost a substantial portion of the money she invested herself, though.
You can also hire people in to provide dedicated training for your troops. There are many businesses out there who provide people with that kind of thing for free.
You can, of course, take steps to ensure their loyalty. The how is up to you, but that is a possible measure you can take.
My hints are still not being taken, I see.
I'll be nice and tell you something outright, then:
You are not restricted to having an administration department, a biotech department, and a security department. I'd hoped you'd all seen that when having Shamus gave you an IT department and having Darius gave you a legal department, but apparently not.
If you want to gain information, consider making yourself an investigatory department. I've already given you the name and typical hiring costs of a man who can lead such a department. You can also use write-ins to try and provide the basics for such a structure.
(You can also try and steal assets to use for your departments, like you did with the biotech assets stolen from the illegal biomod clinic. *coughcoughcybertechdepartmentcoughcough* )