thanks for the guidance, it was very helpful =)
You're welcome! I"m glad I can be of help!
I'd like to point out something that a lot of GMs make a mistake in, and I alluded to it in my previous post. That is that they have a tendency to make the opposition to the PCs fanatical, that they fight to the death almost all the time. We've all done it, and I'm as guilty as anyone for that, maybe more than others in my youth when I felt particularly vindictive against my players. But it's not realistic.
Sure, there may, of course, be adversaries that are going to fight to the death, but that's only a very small number, probably less-than one percent of the enemies any PC in any game may face (even in the Warhammer 40K RPGs). When I run my Shadowrun game, most of the enemies my PCs face like to live, and don't want to be hurt. Getting shot, stabbed, or zapped with magic hurts, and a lot of enemies may not even have DocWagon to help them out. Even some of the more fanatical elements don't want to get hurt, because that means they'll have to heal up before they can be of any use to their cause.
So, when the shooting starts, consider the options the opposition has. If it's better to run away, let them. And when they do, try to put as many obstacles and distance between them and the PCs as possible, because the goal is to get away from the murderous PCs as fast as they can, if they choose to run.
If they have to fight, consider at what point will they decide to quit and run. Usually, I assign someone as a "leader," even if he's not. A group always has someone to key off of, and if that person decides to leave, or is hurt or killed, the others will usually run (though all, or some of them, may like the guy enough to help him). They may even surrender, and beg the mercy of the PCs, however little, in my experience, there is.
I'm something of an armchair criminologist, in that I read a lot about crime (being a mystery fanatic) and I apply this to my games, and if there's anything I understand about the criminal element, it's that they're quite narcissistic. I don't mean that they have a huge ego, necessarily, but that they think mainly in terms of themselves, first and foremost. In Shadowrun, most of the enemies will likely be of the criminal element, be they street punks, gangers, and organized crime soldiers, and most of these aren't fanatical enough to fight to the death. They are quite cowardly, craven, and aren't the kinds of guys who will give anyone a chance to shoot back at them if they can help it. Of course, I'm not talking about the elites, like standard Shadowrunners or Mercenaries, or folks with belief in certain agendas. I'm talking about the kind of criminals that appear in any garden variety blotter report in any given city: Thieves, muggers, vandals, drug-users and dealers, prostitutes and johns, gangers, and wannabes, like criminals who are trying to become Made Men in a syndicate, where they can relax and get some protection and feel like they're big shots. These kinds of enemies will always run in the face of a determined threat, like the PCs, in part because they can't afford to be hurt. Getting hurt costs money they don't have, and if they're injured enough that they can't get cash their in their usual ways, they will suffer for it.
Professional adversaries may fight back, but again there is a point where they will run away if the opposition is too tough for them, or seemingly so. More professional adversaries will gladly retreat in order to gauge their opposition so they can know best how to address them. Retreat, however, is not running; it's relocating to a safer, more defensible area, to regroup and determine what to do next.
A general rule of thumb for me is that in any engagement, with particular exceptions, when a group suffers 25% losses, they will run or retreat. If they take more than 50% losses in the first couple of rounds, they may even surrender.
So do that for your bad guys, and watch how your PCs react. They might find it challenging to pursue, so be ready for that.