you setup the game directory right?
because you should have a save directoy + the map directory...
it would be good if you could tell me which version of qoole your using because each are a little qwirky.
if it's qoole 2.50 then you should've setup your Quake Directory, so you'll have .qle .map in your qoolemaps and your .bsp in your quakeid1maps
and are you compiling or just saving/exporting? because they are also done differently
[edit-]
failing that when everything pops up when you compile, take not if anything fails - because if you have leaks the compile will actually fail and no bsp will be produced, i remember vividly when i first used Worldcraft 3.2 for HL that the levels i created would be full of holes (i dunno why either) and the CSG just would hardly ever compile.
Within the Epic battle of the fates the Shadow and the Angel will meet. With it will harbinger the very fight of good vs evil!