The first day learning curve is steep, but once you get over that, it smooths out rapidly. I too had a lot of trouble following the guide, but trial and error finally taught me what to do. Here is my quick and dirty explanation:
You have two decision trees (for lack of a better term) running concurrently. The first decision tree is movement based and the second is combat based. You must make a decision in both trees for time to elapse. And after a choice is executed, you will get to choose again.
For example, in the movement decision tree, you decide to walk forward which takes 27 seconds. In the combat tree you do whatever you want while walking for the next 27 seconds. If you can see an opponent, scanning them is a good option that often uses up most of the 27 second walking period. Or waiting until an enemy is sighted is a good choice to start a scenario, as is performing a scanner link to an ally. Anytime an action on either tree is completed, you are given the option to execute a new action in that tree. And you can cancel the action on the other tree at that time also. But beware, try not to accidentally cancel a jump or run in the movement tree while deciding what to do with your combat tree decision! And don't set both decisions trees to wait unless you're reloading ammo or in a repair bay.
And sort of graphically:
Overall, a great game with a really good combat system. Punishes you for simultaneous actions and rewards you for using terrain and fire properly. Rookies are all about close combat and the vets try to shoot 'em down before they get close. And always beware the Tesla equipped enemy!
Now I've got to go play again after a 4 month hiatus. This is one of the few games I come back to over and over and over.