You can still install the lines near the cockpit and bow/stern loops after skinning (I've done it on all three of my boats). You just need to melt holes in the skin at the line locations, then drill through them. What I use for melting the holes in the skin is a blunted nail that's a bit smaller than the deck line I'll be using. I hold it with Vice Grips and heat it with a propane torch, then melt the holes. If you're nervous about doing this (understandable), wrap some scrap fabric around a block of wood and test it first, before doing your boat. Once you have the holes melted in the skin, simply drill through the gunwales at the same locations using a bit that's smaller than your deck line, since you want a snug fit for good sealing. For threading bow and stern loops, I made a long "needle" from some thin wire and I use it to thread a thin string that's used to pull the deck line through both gunwales. Near the cockpit, you can just reach inside to thread and tie the lines. In between the cockpit rigging and the bow/stern loops, you'll need to get creative.