When engaging the PTO I have the tractor at idle, depress the clutch, and engage the PTO. If depressing the clutch does not prevent grinding your clutch may be out of adjustment. There should be about an inch of free play at the pedal before it starts to disengage the drive.
On these IHs like the 414/424/444/384 the clutch has two stages the first stage stops the movement of the tractor. Then if you push the clutch pedal down farther then the power to the PTO stops.
Per the above post yes engage/shift the PTO at idle.