You just have to think it thru.
The engine is running and turning all the time, bad bearings only make noise when they're turning.
So you push the clutch pedal in and act on the master, the master acts on the slave, the slave pushes the clutch fork towards the pressure plate. Now the static fork has to press in the fingers on the rotating pressure plate, it makes this interaction with the throw out bearing. The only time that bearing turns is when the clutch is in. When the clutch is in it also disconnects the engine from the tranny so the tranny internals will stop rotating as long as the car is stopped. So, if it's bad it will only make noise when the clutch is pushed in.
When you let the clutch out in neutral the TO bearing moves away from the PP and stops turning. The engine engages the input shaft on the tranny and spins it, because the tranny is in neutral the output side of the tranny remains stopped. So now the TO bearing is stopped and the input shaft bearing is spinning.
Basically if the clutch is in and you have noise then the TO bearing is bad, if the clutch is out and you have noise the input shaft bearing is bad. As a rule only one spins at a time. However, if you get the car rolling and engage a gear then put the clutch in both will be turning, the engine will be turning the TO bearing and the wheels, via the tranny will be turning the input shaft bearing.
Get the car coasting a good clip somewhere safe, kill the HVAC, stereo, and engine to quiet things down. Now, with the clutch held in play with the shifter and change gears. The engine is stopped and because of that so is the TO bearing. If your input shaft bearing is screwed it'll change pitch when you change gears because the rotational input from the tires is relatively constant and the rotational speed of the input shaft is a function of the gear ratio. You'll also hear a whirring as you engage the gears, that's the synchros and pretty normal. When the input shaft bearing goes bad chances are it'll take out the input shaft seal too and you will find oil residue all over the inside of the bellhousing, let that go long enough and it'll take out the clutch.