How does marking work in MGS 5?

I'm a little confused about the specifics of how marking works in Metal Gear Solid 5 Phantom Pain. I have gone through the binoculars tutorial and so understand the basics of aiming and marking but the other details are not really mentioned anywhere. For example are there any time limits around how long a marked enemy stays marked, or if they are out of line of sight or beyond a certain distance? When battling Quiet for example she appears to randomly become unmarked and I'm not sure why that is? Also is there any way to mark with an aimed weapon as oppose to using the binoculars only?

You can only mark with Binoculars, because it shows a lot of info once recruiting is available in the Mother Base.

They should stay marked throughout the whole activity. Quiet is an exception because you know, she is hiding from you and running really fast around the place to try to get a better shot to your head.