Adaptive rules
Have you cosnidered using the mount rules? As the flying character is providing the movement for both, consider that character as a mount for the other. This is the base from which the many options for how they are moving come into play. Next, substitute the character's standard movement for the fly spell movement rates. Now, we have two characters in the same space moving at the same speed in the round. The "riding" character will have to delay their action to match that of the "mount" character. There is also the question of actions. Obviously, the "mount" character uses at least one action for movement (even if it is hovering). The "rider" character does not need to do such a thing, but if s/he has any mounted feats, they may come into play if they make sense based on the characters form of connection.
Let me delve into the connection for a moment. One of the two must hold onto the other, unless there is some form of riding utensil in use. Under basic rules for actions in the PHB, holding something is a non action action. Actions are spent in the getting of whatever is being held. So, common sense kicks in, if two hands are used for holding, then you have no hands to use for making actions. If one hand is used for holding, then I suggest you bring in the climbing rules for how to adjuticate the check to continue to hold while you complete the action you desire. Although it is not exactly the same, it is similar and makes a little sense. My example: both characters (one climbing and one holding on while flying) wish to make a simple attack during the round as part of their action. Would it not be similar for the flying character to grasp onto something while they swing that weapon as for the climbing character? Yes, there are two distinct differences (the climber is not moving and can use feet as an anchor point as well), but they are close. As DM, you can arbitrate a penalty that seems commensurate with the difficulty of not having the feet to use and for the moving part.
I would also like to address cover briefly. The only time cover will come into play, is if one of the two characters is physically obstructing the line of sight/effect to the other. If one is, then determine the percentage of cover and assess the AC bonus to the other character. If one is not "in the way" of the other from the source's (this would be a bad guy) point of view, then there is no cover granted. Cover is a situationally based bonus and in three dimensional combat, may not always come into play as a flat rate. It may need to be adjusted with each passing player or NPCs' turn.
There are many ways this situation can be handled. Once you have decided on a way, make sure it is consistant with any future situations that arise. It will be very space and time consuming to continue to puzzle this out without knowing exactly how the situation unfolded, but I have addressed some of the ways the rules can be adapted to support the situation in a logical way. Are they specifically for that situation? No, but they can make sense from a point of view and they lay down a framework to begin adjuticating how the actions support the situation. The rest is up to each DM to adjuticate the situation as it unfolds in their own game. All of these rules adaptations will probably bog down the combat a bit, so, you may want to consider informing the characters that you are assigning an abstract set of bonuses and penalties for both them and the bad guys to adjuticate how difficult the attempted maneuvers are in order to speed up the combat. Again, this is another decision for each DM to consider given the composition of their own group.
I hope this helps somewhat.