Did you or are you taking one or both of the cylinders out? It's a real pain to get the tubes screwed on the rams if you have the ram bolted in already.
I have found that screwing the tubes on when the system is out of the car is the best way to insure you don't kink the lines.
I also used tie straps to hold the lines to the rams so that they do not rub against the outer body or get yanked when the top is going up or down. It worked well for me. Just my .02 cents. I've got the whole system out of the car and still connected.
Hope all is well. Now that the weather is getting better I am starting on my project again...It never ends. I've got the rear Driver quarter, tail panel off the car and the pass floor is getting some work also. Need to buy the sheet metal and continue.