So, how do you time a deep cut? Like I mentioned above, the first step is to just start making hard, sprinting deep cuts when your favorite thrower catches the disc. A lot of times, just starting from a standstill at the back of the stack and sprinting deep when a handler catches an upline cut or a cutter catches an under will give you the couple yards of separation you need. However, against smarter/faster/better defenders, you'll start noticing that those simple cuts aren't enough. In order to keep getting separation deep, you'll have to anticipate those cuts and be setting up your deeps by pushing your defender under. This not only gives you more space to cut into, but it gets your defender off balance and makes it more difficult for him/her to anticipate the deep cut and get in your way.
So, now that you're an awesome deep cutter, how do you take the next step and turn those deep cuts into huge unders that propel your team's offense? How do you know when you're supposed to stop cutting deep and come under? The answer is simple: look at the thrower. As a thrower, when you see that deep cut going (especially when you catch a power position under or strike cut), you need to do one of two things: either (a) throw it deep or (b) pump fake deep. By doing (b), you not only give your receiver a clear signal that they should stop their cut and come under, but you get the whole defense to bite deep. Any defender watching you sees you wind up and assumes it's going to be thrown; a good fake will even draw some up calls from the sidelines, which will help your cutters get open more as the defenders pick their heads up looking for a huck in the air.
As a cutter, when you start making your deep cut, you should ideally be burying your head and running full speed, so that you can beat your defender. But, you also need to be able to see the thrower and look for the disc going up (allowing you to get a better read on it than your defender) or the pump fake, telling you to come under. So, the next step to effective cutting is working on your timing so that you can peek back at the thrower and see them either throwing the disc or giving a pump fake (rather than running the whole cut with your head over your shoulder, which slows you down significantly).
Hopefully, after reading this, you have some idea of how to build and learn effective cutting techniques. As an example, I've included a .gif below, from an Ironside (Boston area men's club team) vertical stack progression. It shows pretty much everything I talked about above - only possible improvement is that the cutters are running with their heads looking behind them (as opposed to timing a "peek" to see the thrower).
Make sure to use the pause and slow-mo functionality to really get the most out of this clip. You can see that the first cutter (George Stubbs, a Callahan award winner) starts making a deep cut as the previous cutter catches an under. When he gets a pump fake, he turns and plants under. Meanwhile, the next cutter, Peter Prial, is mirroring his cut, pulling his defender under so that he can make a deep cut when Stubbs catches the disc. Though the huck is thrown to Prial, I am pretty confident that if Stubbs had instead thrown a fake, Prial would have come under for a 30 yard gain and the next guy would have been cutting deep. That's just how good, fundamental cutting is done.
[Side note: if anybody has a higher quality .gif of this play I would love to get it. Can't remember for sure what game this is from and I can't find a higher quality version online]