Do it while the tractor is shut off (in all the cases I know of anyway) I've owned dozens of tractors. Worked on HUNDREDS more. In every case I can remember, there needs to be about 1" of free travel in the clutch pedal before you start operating the clutch mechanism.
I'd HIGHLY recommend consulting your particular tractor's manual (Owners, or better yet, SHOP manual) for the correct RECOMMENDED free play.