Last night I ran a combat in a plane that's a mix of Fire/Air/Shadow. Basically movement works like the plane of air where you chose you own "down." The combat especially was a tad confusing for the players to keep track of the enemy locations but overall there was the confusion on what sort of movement/combat maneuvers were allowed for the players w/out fly movements. What do you suggest to smooth out combat/make it viable for parties with not a whole lot of ranged options? As well something came up where a monk used Open Palm technique to knock a flying creature(Yrthrak) prone. To which I was like "Uh...." On the spot I decided that it's fly speed would be halted and that it lost its attack but what would be the effect of being knocked prone from an ability on the plane of air especially to a creature with a fly speed. Thanks for any suggestions. 

For the prone rule, i would argue that the creature falls (I'd use Xanathars 500' rule) and has to use half its movement to stop falling.  This could effectively take it out of the fight for a while as it would have to climb back up to the fights level.

Regarding the 3-dimensional combat, I've done the following:

For Battlemap play, I use clear dice boxes or other markers to show relative simple positional heights above or below a "zero" plane ("above" and "below" being the only thing communicated) and track the actual distances as the DM, and then make quick math rulings on the distance when a PC asks about distance to a target.  For TotM play, I just do the tracking.  I don't really know an "easier" way than that.

On a plane with no gravity and thus no real concept of a direction of "down", e.g. the plane of air, making something prone wouldn't make the creature move anywhere, and would just cause its rotation to change. You could argue that instead of "prone" they are disoriented, and thus take half their movement (like getting up from prone) to re-orient themselves again.

Maybe I’m just out of the loop, but I thought the plane of air had a distinct “down” you could fall in the direction of (there are amounts of solid ground, so that’s how I would assume you could stand on it).  But if you are running it as a gravity-free area then I think your ruling is fine.

The plane I had the party on did have subjective gravity but I couldn't find anything about how choosing it changed movement for creatures with flying(Ie changing the gravity and "divebombing" everything). As for the "prone" I'd imagine maybe it would half its speed since it could chose the direction it fell. Another question I guess would be does a walking creature's speed change based on direction in mid air or is it moving as fast as it could fall(500' a round)? So in that case would a creature knocked prone that doesn't have a flying speed move "down" at 500' a round? I guess that makes it kind of worthless ability wise in subjective gravity areas that are open sky. I think I'd rule a sort of "round of disorientation where you can't chose a "down" so you just float. Thanks for the insight though I wish there was something printed out somewhere.

Zero Gravity

Movement in zero gravity (also referred to as zero-g) is not the same as flight. Controlled movement is difficult without some form of propulsion, and creatures without something to push off from often find themselves floating aimlessly. A creature in a zero-gravity environment can’t take move actions to move its speed, crawl, or take a guarded step. If a creature is adjacent to or in the same square as an object (including a wall, floor, or ceiling) or another creature one size category smaller than itself or larger, it can take a move action to push off that object or creature, moving at half its land speed in a direction of its choosing (as appropriate); if that object or creature is movable, it begins moving in the opposite direction at that same speed.

• Moving in Zero-G: A creature that moves in a given direction continues to move in that direction at the same speed at the beginning of its turn each round (without taking any action); it must move the full distance unless it is able to change its motion by latching on to an object or creature, pushing off in a new direction, or creating thrust of some kind (all of which are considered move actions). If a creature runs into a solid object during its movement, it must succeed at a DC 20 Acrobatics or Athletics check to safely stop its movement; failure means that creature gains the off-kilter condition. If a creature runs into another creature during its movement, both creatures must each attempt a DC 20 Acrobatics or Athletics check to avoid gaining the off-kilter condition. A creature anchored to a solid object (such as by the boot clamps available with most armor) receives a +4 bonus to this check. An off-kilter creature in a zero- gravity environment can steady itself as a move action that requires a surface to grab on to or some method of propulsion; alternatively, that creature can throw a single item weighing at least 4 bulk (for Medium creatures; 2 bulk for Small creatures) to reorient itself and remove the off-kilter condition.

  If provided with sufficient handholds, a creature with a climb speed can move along a wall at full speed, as can any creature that succeeds at a DC 20 Acrobatics or Athletics check. Creatures that fly via methods that require an atmosphere, such as wings or turbofans, can’t use their fly speeds in a vacuum; once they reenter an atmosphere, they can recover and get their bearings within 1d4 rounds, after which they can fly normally. Magical flight and methods of flight that provide their own thrust, such as maneuvering jets, are not affected. A character in a zero-gravity environment can lift and carry 10 times her normal amount.

• Weapons: Thrown weapons have their range increments multiplied by 10 in zero-g. In addition, all ranged weapons no longer have a maximum number of range increments—their wielders simply continue to accrue penalties the farther away the target is.

Google is your friend. This is from Glasstop Games with an OGL.