Ok. I hope you understand how a level pack/episode is structured in JK. JK loads GOB files that have a folder like structure with the actuall levels in a jkl folder, then the scripts in cog folder, models in 3DO, etc. To make an episode/level pack you have to make a project folder which can be considered a GOB file, only it ain't a file, but a folder.
Now, J/ZED creates JED levels/files which can only be read by J/ZED. The JK level would be a JKL file that is stored in the subfolder jkl which is found in the project folder. When you want to test your level, you have to save a jkl file, then run JK with a few switches that points to your project folder (usually J/ZED creates a bat file that you can later on double click).
If JK crashes, then either it is missing resources, or you've got too many. Or something else is wrong either script wise or level wise (one too many vertices here, incorrect normals there, etc).
Give more details and we'll see what we can do. Come on over to JKHub and present your problems there as well. That's where most of the JK Editors have fled to.
/Edward