I have a DP 1.25 MDD and I have both the combo and an added superdrive. I would recommend keeping both in so that you can have the added benefit of the faster combo burning speed and also the ability to copy from on e CD to another.
To add the superdrive however, you must make the combo drive the slave (i.e., take the combo drive out, put it in the bottom bay, pop in the superdrive in the top bay and reconnect the cables, which should be set to cable select so that the superdrive becomes the "master" drive). Without doing this, or with just putting the superdrive in the lower bay and connecting the cables up (which will make the superdrive the "slave") your G4 will not recognize the dvd burner as a superdrive and it won't work.
Oh yeah, make sure to get a pioneer (branded or unbranded drive), or the G4 will not think it's a superdrive.
- reaper