Been playing this this morning, this is what I've surmised:
First thing's first - the more you press 'h' the more help you get.
Create a squad with the triangle gesture and go massacre the virus near the start. Make an engineer and it'll harvest up those souls and turn them into Darwinians. Be prompt as otherwise the souls will fly into the sky and be lost. Make an officer near the Incubator (you can tell what a building is by hovering the pointer over it for a few seconds), and make him point where you want the little guys to go - an officer can only point from one location to another, so the best way to do things is to make another officer at the other end and make him point somewhere else - kind of like ant trails. So you'll have a continuous trail of moving purple dots like a road. You'll get it when you do it.
You can only run four programs, so don't be afraid to terminate programs if you don't need them. You'll need an empty slot to create more officers.
e.g. enginers can be terminated and run from somewhere else to save time in making them go somewhere.
If you place a squad somewhere, and put the camera on the floor where they are, you can aim into the air first-person style. Select a squad and change their weapon to rockets with the rocket gesture, and you'll be able to fire rockets into the air - very handy.