This is a pretty good thread.

I don't have a method I use all the time though. For some of my levels I just made the layout while I was in JCS, so I didn't use Paint or paper. I have made some layouts in Paint though. Those levels are Apple Land (without the bottom level with the water though) Cold Waves, Heated Pipelines, Space Station: Milaria, Diabolical Darkness and The Light Returns. I've made some layouts on paper before, but none of my good levels were made on paper. A part of Death Castle CTF(my second CTF level) was made on paper. But most of the time I start making the layout while I'm in JCS.