The Eternabond will seal up the skylight cracks - at least until you decide to get a new one. I would not have messed with it - but I guess that is a moot point now. .
You can buy Eternabond in 2", 3 and 4 and 6" wide as well as 18" wide if you are really good at installing it! I would have placed the 4" wide Eternabond near the low section of the roof, so the seams are out of the standing water. What water stands in the center of the tape will not matter, or leak in.
Good luck!
You might also want to check out EPDM roof sealant, I made a post about it a while back. It is working great on my RV, and will fill in low spots.
Fred.