It shouldn't make any difference to the fuse if you hit the up button when the window is already up, or down when it's already down. The motor is not going to draw any more current than it normally does just because the window is at full top or bottom.
Based on the info you have provided, it definitely sounds like you are drawing too much amperage through the window circuit, and the most common cause for this would be a short as you mentioned. The short could be in the wires that feed power to the regulator motor, or it might be in a shorted motor. Since you say that the motors work (?) with a new fuse, then it seems more likely that you are dealing with a shorted wire problem. The question is where is the short ?!
You will need to do some circuit tracing to locate it, but there are some common sense things to consider before you start ripping the truck apart. You want to think about those areas where the wires would be subject to wear, which over time would chafe the insulation and eventually allow a bare wires to touch another wire or another ground point. Areas that could be a problem would be where the wires flex (inside the sheath between the pillar and the door), or where there's vibration or movement (the window moving up & down inside the door and possibly rubbing against the wire harness that goes to the motor). These are the places I would be concerned about. Since you are not dealing with a window that simply won't work, I would not be suspicious of a corroded wire or ground point, because that would simply mean the power window would not operate because the circuit was no longer closed (grounded).
You say that you are blowing fuses when you use the buttons for the rear window on the center console. You should make sure that the buttons on both rear doors actually are making the window move UP and DOWN without blowing a fuse. If that's the case, then you can eliminate this part of the circuit as a potential short location. However, if you find that the fuse is blowing when using the front OR rear buttons, then the short must be located inside the motor (again, not likely since they are working), or the short is located at a point BEFORE where the front console and rear door window buttons separate from the circuit. In other words, both front and rear buttons causing a blown fuse indicates that the short is common to the harnesses that feed both the front console and rear door switches.
Next, you need to check if the left or right rear window, or both windows is causing the fuse to blow. This will tell you that the short is located between the window button that is being pressed when the fuse blows and the regulator motor for the window which is blowing the fuse. If both windows are causing the fuse to blow, then you can deduce that the short is either in the switches (both of them... which is unlikely), or it is somewhere in the harness between the switches and the regulator motors of both windows. Since the rear window wire harnesses split up not far from the center console, the short will have to be located pretty close to the console itself, before the left and right harnesses split apart. Since there are no moving parts in the center console that I can think of which might damage the wires, I think it's unlikely that you will find that BOTH rear windows are making your fuse blow.
Once you have narrowed down the culprit window, you can use a multimeter or Ohmmeter to confirm that there is a short between the wire(s) at the switch and ground. Disconnect the wires from the switch and put one probe of the multimeter on the end connector of one of the wires and the other on the other wire that forms the circuit going to the regulator of the suspect window. If you get an indication of resistance (probably full deflection, infinity or overload), then there is NO short between the two wires. If you get 0 Ohm (Zero) resistance, then you have an open circuit, therefore a short between the wires. If not, next put one probe on the end connector of one of the two wires and the other probe grounded to the chassis, preferably the door itself. If you get some resistance (again, full deflection or infinity), then there is no short in that wire. If you get 0 Ohms, then that wire is the one with the short. At this point the last wire to be tested should be the cause of the short, so put your probe on the end connector of the last wire with the other probe still grounded and confirm the sort (0 Ohms). One you know which wire(s) is causing the short you can start tearing stuff apart to visually examine the wires and locate the damage. When you find the spot it is considered "best procedure" to replace the entire run of wire because there could be some heat generated damage that is just an accident waiting to happen. That call is up to you. If it appears that the damage is very localized and you don't see signs that the insulation has melted anywhere else, (including ADJACENT wires which might also have been affected if the short was located in a tight bundle of wires), then you can consider a localized repair using heat shrink insulator rather than electrical tape if possible. Remember if the repair is inside the door, there is water, salt and crap that get in there which will easily get past electrical tape ! You'll need to cut the wire at the damaged spot anyway to clean and remove the damage, so this is when you slip on a length of heat shrink before you SOLDER the wire back together. Do not simply "twist' the wires and expect that to last ! If you have to remove a fair bit of wire there might not be enough slack wire in the harness to rejoin and you might need to add a length of new wire, so make sure it is of equivalent gauge or you'll be creating a "hot spot" that will come back to haunt you later, and you will be doing the exact sam repair all over again.
So before you get settled in for some circuit tracing, you should buy yourself a few packages of fuses because you go though several
Also, you should note that when doing this kind of hit and miss circuit tracing for a short, you are in effect allowing over-current through the circuit for a very brief period (the time it takes for the fuse to blow, which is NOT instantaneous). There is the possibility of overheating the wires in the circuit with repeated attempts, particularly if the over-current happens at short intervals and the wires/insulation don't have a chance to cool. So allow a few minutes between attempts for that to happen, which will probably be the case since it will take some time to replace the fuse... If this was an aircraft, we would use more specialized and sophisticated equipment (time domain reflectometer and test set circuit breakers) to prevent this kind of potential damage. You might want to buy fuses that are the next gauge down from what is supposed to be used for the circuit, so that you don't damage any of the wires through overheating by repeatedly allowing high current though the circuit, but this is probably overkill for your application, and you would need to know the actual current draw of the circuit to pick a suitable downgraded fuse anyway...
So, in summary:
1. Buy some spare fuses
2. Check operation of left rear window using front console button --> Problem YES skip to 7/Problem NO continue
3. Check operation of left rear window using rear door button --> Problem YES skip to 7/Problem NO continue
4. Check operation of right rear window using front console button --> Problem YES skip to 7/Problem NO continue
5. Check operation of right rear window using rear door button --> Problem YES skip to 7/Problem NO continue
6. With a culprit window and button identified, determine if fuse blows when window raises or lowers
7. Examine the suspect wire(s) from known good location to regulator motor looking for short.
Hope this helps !
Let us know how you are doing, and if you are having fun
Kev