The transition line is not that evident, and thatís the whole purpose of using graduated filters. Obviously you know this.
I donít have your problem, but if I did, here is what I would try: it seems like your Cokin Z-Pro holder has extra slots for using more than one filter at a time. If so, I would cut a piece of black board the thickness and width of your filters with the height just to cover the filter's darkest area, maybe a little higher. This would allow me to slide it up and down, just like a filter.
When ready to shoot, place the graduated filter in the slot closest to the lens. Next, insert the black board into the second or third slot in front of the filter and slide it down, placing its bottom edge where you want the transition to begin. You should be able to see it through the viewfinder without a problem. Now, make sure the filterís transition line is even with the edge of the black board, sliding the filter up or down as needed. Next, remove the board and shoot. You could probably substitute the black board with a second filter, thus saving you the trouble to cut it.
This would probably add time to the capture process, but with practice, it should be fairly quick to do. Just an idea.