The way I did it with Oblivion was to generate an image file from your ESP or ESM using TESAnnwyn to export the terrain(with the -g option to overlay a cell grid). I have successfully used TESAnnwyn with Skyrim to CREATE (import) a worldSpace terrain with vertex coloring, so that app SHOULD be able to export one back out again. The instructions for TESAnnwyn are fairly confusing, so if you need help as to what command-line to use with which options - lemme know. (I DO know I had to use the FO3 settings, NOT Obliv's)
Now you should have a color map with black gridlines... I used Photoshop to insert numbers into the image at various intervals, so to see an area's cell number quickly. My worldSpace is as large as Skyrim itself (several quads), so it took a little while... but it was worth it for my project, as I have several region types and areas. Then, with that exported map, I traced colored pencil-lines over the border cells where I wanted to place my region - then in the CK you'd open the region editor. Looking at your marked-up map, you should be able to see which cells require a region marker (indicating a corner)... mouse-over cells in the region editor to see their cell numbers.
An easier way, if you have a relatively simplistic worldSpace, would be to just make a basic square or other simple shape. In the CK, locate which of your cells are the 'corners' and write them down (I don't remember it allowing one to switch between region-editor and render-window)... then assign them in the region-editor.
svcks... I know - but I'm not the one who designed the CK/CS. I agree that it should have SOME kind of basic terrain overlay - even just water vs land would help.