I'm glad you asked about this, urbanagrarian, as I noticed the same thing with our Hova and auto egg turner.
I've been using a small watering can whenever I need to add more water. The spout of it is small enough to fit between the rows of the turner without getting the eggs wet. I'm just doing a trial run with some of our own eggs right now, just to get the hang of incubating and how the Bator works.
Cyn,
I had the same idea of coloring the troughs to make them easier to see/easier to fill. Will be using some aquarium tubing on the next "trial run" to add water to the bator so I don't have to keep opening the top to add water.
Dawn