You'll learn along the way, but a good start would be to not try to take out everyone. Just take out the ones you really, really need to to get to your objective. Even then, it's often better to just sneak past the enemies. It's difficult and risky but you'll learn that way. Marking the enemies is good though, continue doing that.
As for me, the above method works sometimes. More often than not I get spotted during a mission, but said method usually gets me quite a long way. I could probably improve my performance by misleading enemies, for example by using empty clips and decoys more, but I'm not at all comfortable with the small time window the clips give.







