Normally, you will write CLIPS files, and load (or batch) them into wxCLIPS from the File menu. If you find a bug, you can change the file in your editor and reload.
Note that there is a difference between batching and loading. The CLIPS load command only handles definitions, not function calls. However it does more error checking and is faster than batching. The purpose of batching is to allow function calls to be included in your files, and it is also the only way to automatically load CLIPS files from the command line (see below).
The best strategy is to have a small batch file which contains load commands to load the bulk of the application, plus a few function calls, and it is this file which is batched.
If you want to rerun a GUI application, but there are still windows lying around, you can use the Clean up windows menu option from the Application menu, or call the clean-windows function.
If you define a function called app-on-init (see next section) you can use the Start application menu item from the Application menu, which calls this function automatically.
Debugging can be made easier by typing (watch all) to get a trace of function calls.