Yes you can all that you are required to do is to release the pokemon to a open space and right click with the mod. From there you will see a guide that you can choose the new pokeball your pokemon will change into with out the need of actually having the ball in your inv.
I noticed that when i reloged into tge emerald server around 3pm yester day that when using payday, i did not receive coins as a result. Im just wondering if the rewards of payday were disabled.