Pushing the clutch pedal in half way disengages the drive clutch. Pushing it in all the way disengages the PTO clutch.
The way it works is there are two driveshafts coming out of the clutch pack, one inside the other, one for drive and the other for PTO. The PTO driveshaft is inside the drive wheel driveshaft. The clutch pedal is connected to the release for the drive clutch, and the releases for both clutches are connected, but there is some play between them. So when you push on the pedal the drive clutch release moves first, then when it has moved enough to take up the play the PTO clutch release starts to move. That amount of play is critical, and it is set by a gap between the clutch release fingers on the two clutches.
Right now it sounds like your gap is too big, so pushing the clutch pedal in all the way doesn't cause the PTO clutch to release all the way. Sometimes all you need to do is adjust the pedal so it travels further. I suggested that because it's a lot easier than adjusting the clutch gap. To adjust the clutch gap you're going to have to take off that loader you just put on because the loader mount plate covers the hole in the side of the transmission you use to adjust the clutch.