It's not that hard, I like to use gloves so that I don't get fingerprints on the encoder. You don't really need to remove much for covers, I don't when I service machines. It is easier to get at with the top cover off though.
It's simply a matter of removing the spring from the left hand side, unscrewing the "plate" holding the encoder on the right, then transfering the "plates" (sorry not sure what you'd call them) attached to both ends of the encoder. You will have to move the printhead out of the way to get at the right hand side. I like to attach the left hand plate to the new encoder at this point. The encoder with the black dot should be on the right hand side. Make note of the orientation. Before you attach the right hand plate to the new encoder, slide the right side end of the encoder into the trough and push the print carriage to the left past the end of the encoder so that you can pull it all the way to the right. Reattach the plate on the right and screw it in place. Then pull the encoder taut from the left, making sure it's in the trough, then attach the spring to the left plate.
Try not to move the print carriage too much before you verify that the encoder reader is in the correct position. This is the sensor located at the back of the print carriage that straddles the encoder. There's a small screw you you can loosen to make adjustments. Make sure that it is not rubbing on either side of the encoder. Then you will have to do a limit position.
Process is here:
I hope that somewhat makes sense..
EDIT: I really should have just linked this video... :