You can also enable per page skins in site settings and then you can specify a skin per page or use the default skins for most pages and specify a specific skin on some pages. You can also organize your css files so the different skins share the same files except for the column layout css.
If you are using the latest mojoPortal version 184.108.40.206, the skin css has been re-organized to make it easier to find things, the column layout part is near the top and has comments identifying it. If you upgraded, the new updated skins are located at /Data/skins, but the ones used by the site are at /Data/Sites/1/skins so you may wish to copy the ones from /Data/skins into the site specific folder to get the new versions.
So you could move the column layout css into separate files per skin but other than layout use the same other css files for all the skins.
Hope it helps,