I just went through putting in new cylinders.
1-Put the top up.
2-Unbolt the top single bolt from the piston rod.
3-Loosen the two bolts that are on each side of the cylinder bolt(good point Kevin, mark where they were before you loosen them). After they are loose you can move the cylinder and it will move the outside bolt into a position where you can get a wrench on it.
4-Remove the inside cylinder bolt. This one is a PIA!!
5-The inside bolt even though loose sometimes cannot be removed because there isn't enough room to back it out. If this happens you'll have to monkey with it until you can pull the cylinder out.
6-Remove the hydraulic hose from the cylinder.
After I put in new cylinders I used ATF in the pump. All I did was fill the resovoir about 75% then put the top up and down(with the resovoir plug off) and refill the cylinder each time until everything was full of fluid and all of the air was out.