I know it can be frustrating a bit, but keep in mind that the more runways (ships) you use, the more it also effects frame rate, at least in my experience, so I try to keep it down a bit. I have found that the visible runways are a bit short, and I usually put them end to end.
I wish we had access to the parking areas we see in the sim sometimes. I usually put another runway parallel if i wanna use a parking area.Also keep in mind that hangars/revetments don't recognize the runways and will be sitting on the ground. Not much of a problem on the lower runways, but keep that in mind. ive used them before successfully.
The reason they have one wiht alot of elevation is for use with uneven ground. It's kinda hard to find flat territory on some maps....I think.
I've used trees to mark the sides of the runways before, and there are some white panel markers in the objects list that make great outlines for runways. Comes in real handy on those quasi-invisible default desert runways. some have used the campfires as well.
on my version of fighter one on Guadalcanal, I used palm trees to roughly mark one side of the runway, also parked some planes in revetments just off the edge of it. I didnt use "set" so the planes all took off in staggered formation. You can see the edges of the runways marked if you look close enough, but I found I could place the invisible runways better if i originally used a visible one, which are a bit shorter I think. Then I just changed it to the invisible one. I cant remember the numbers. I'm old.
I sometimes put marsden matting on grass runways or taxi ways, but you gotta be careful about taxi-ing off the sides. I found that carrier planes seem to be able to roll off the lower marsden matt runway without usually getting any damage because of their tough landing gear....apparently.
Dont forget about the direction you place the ship/runways. Keep in mind this was an afterthought solution at the request of the community. It was apparently the only way they could do it, and it involved a bit of work. They never tried to say it was a total solution, but it will do for building out own runways. Maybe there will be more airbase building resources in the new SOW series.
Take a deep breath man.