Good question as I intend to add this stuff to the FAQ, but I don't think this has been explained yet. So I'll explain the way it works now and we can discuss and you can test with a little more knowledge.
For cover, you basically have 3 types of players - LBs, CBs, and Safeties. Safeties are also designated as SS and FS which is important. You also have the 5 possible target locations - Very Short (behind the line), Short, Medium, Long, and Deep (>20 yards). You can have 3 types of receivers - RBs, TEs, and WRs - along with their certain slot location distributions set on the formation which can be thought of as "routes".
The most simplest way to look at this is: LBs will cover RBs and TEs and their routes. CBs will cover WRs and their routes. Safeties will cover zone locations based on the Cover settings. We all know how complicated football settings could be, so if you want to think of this in football terms, I would say this is closest to a Cover-2 with some adjustment on the Safeties play based on the Cover settings. The easiest explanation is that CBs and LBs play man coverage and Safeties play zones.
What this means is that CBs and LBs will tend to cover where their target goes, so even if you have Long cover, these guys will try to cover their players even if they go short. How well they cover them short can be adjusted, but they essentially don't just sprint down field because the Cover setting is Long.
While the CBs and LBs follow their receivers settings, the FS and SS follow the Cover settings. For Short cover, the SS will mostly play Short and the FS play Medium. For Medium cover, the SS will mostly play Medium and the FS split between Medium and Long. For Long cover, both will mostly play Long.
Where it gets a little more complicated is when you have mismatches. For instance, let's say you have 1 CB and 3 WRs. If you have extra LBs, they might be put on WRs, but if you do not, then you will have less coverage. This can happen between different formation match ups or when defense is blitzing. A lot of the passing balance I was working on was to take account of these mismatches. How well a player is covered, depends on how many players are in the targeted location as well as how well those players match up ratings-wise, and we'll also figure out which defenders are in on the coverage. Its more complicated than that, but that's a simple way of understanding it. Once the ball is thrown to the target, only those defenders that were in on the cover can defend the pass and be in on the initial tackle after the reception.
All of this is able to be adjusted in many different places, and there may be some places we need to tweak, but for the most part, this should help explain some of the results a little more. Also, you should see some synergies like if your Cover is Long, maybe more short passes are made but they don't get as many long runs because there are more people between them and the end zone, but if your Cover is Short, maybe you prevent more short passes, but there aren't as many defenders to get through on the YAC.