Marking halyard - yes. We had thin halyards which were fat only where they hit the cleat when the kite was right up, so that kinda marked itself.
Patches - People have different views. Two patches means a longer sausage and probably means a slower hoist for that reason. Three patches might be expected to be harder, but if everything really works we found it fine.
Patches - we put the ring of the bottom and middle patches on strings. 450mm and 300mm from memory. This had the effect of separating the three patches as they go into the chute. I do not recommend having the patches moved so that the corners are all equal when you stagger the patches. This is because if the corners are all at the chute mouth at the same time they may jam up and cause difficulties. It is also because (we think) you actually want the head to go in first, followed by the clew and then the tack. If the head is furthest out, the motion when going upwind may pull it out. Similarly the clew, esp if the sheets get in the water. With the head in first, when you hoist, you pull the head section back past the other bits of kite, true, but we think this is better than the slower (though probably less trawl-risky) two patch approach.
Three patches became the norm in 2005, but I guess there is no obstacle to 2 patches, except for sock length.