There are MANY bearing in the transmission. Input shaft bearings, Output shaft bearings, Differential bearings. It's not common for any of these to fail but it does happen. You also have your throwout( or release) bearing for the clutch and some cars, but not your model, have pilot bearings. Pilot bearing are generally reserved for RWD and 4x4 vehicles and some, but not many, FWD's
I don't know how much you know so I'm just going to type this out anyways. You can tell me to shut up if you want.
The input shaft of the transmisson is the same thing that your clutch disc is mounted to. It's where the engine's power is input into the transmission. That shaft will spin the same speed as the engine itself(when the cluch in engaged) so any problems you'd have with that in regards to bearings or any other noise, would be directly related to engine RPM. The throwout bearing is also riding on that shaft.
The output shaft is what the input shaft drives. The output shaft is also connected to your differential. It will make noise based on wheel speed regardless of if your clutch is engaged or disengaged. The speed of the output shaft is not the same speed as the wheels, but it's a direct relation to the speed, depending of the "final drive" ratio of the transmission.
To make things more confusing.....
the output shaft is ALWAYS connected to the wheels so it will be spinning in relation to wheel speed no matter what.
The input shaft is kinda "floating" so to speak. If you have the clutch engaged but your shifter in neutral, the input shaft will be spinning the speed of the engine but will not be making contact with the output shaft so your car will not move.
If you have your clutch pedal pushed in(disengaged) and your shifter is still in neutral then your input shaft will not be moving at all, and you wont move.
If you have the gear shifter in any gear, and your clutch disengaged, the input shaft will not be moving as it's connected to your vehicle's output shaft physically by the gears on the two shafts and not connected to the engine (due to clutch disengagement), and you don't move.
And Finally, when you are in gear, and you engage the clutch, the input shaft becomes physically connected to the engine (by the pressure from the clutch plate springs squeezing the clutch disc between it and the flywheel.) since the gears on both input and output shaft are touching, the car starts to move. The speed of the input shaft is the same as the engine while the speed of the output shaft is related to the size difference between the gears on the two shafts. The output shaft will spin faster as the cars speed(tire revolution) increases.
If I've confused anyone...cool.
I'm sure I'll proofread this and edit stuff that I see wrong........