You can definitely use your own folders, but you have to make sure that you reference the Web Connection folders from your application folders. You need to ensure that the path exists to \wconnect\classes and \wconnect. Further some of the Web Connection tools (like the Console) will only run out of the Web Connection folder as they depend on content in subfolders (like templates and scripts etc.).
However, for project building purposes it's perfectly fine to use a custom folder to hold your PJX, main and process files as well as any app depended classes.
+++ Rick ---
from Geneva, Switzerland