By far the easiest way to thok-barrier a level is to create an enormous square sector before you make the level, set its floor height to equal its ceiling height, and draw the rest of your map inside that. You would subsequently want to mould the edges of the square to fit your level, since a thok-barrier of varying thickness looks a little odd.
It may be too late for you to do that now, of course. Some quick experimentation in Doom Builder seems to suggest that drawing a large sector entirely around your level is safe (i.e. makes your existing one-sided linedefs two-sided and sets the sector references correctly). It's been a long time since I've used WadAuthor, but if memory serves it won't do that correctly. Anyone know otherwise?