See, there are no dumb questions !
Development structure is where you put your java files, html files, all other resources. You will compile java files and .class files will be generated here only
While, Deployment structure is where you will copy all your resources from development structure which will include .class files and not .java files.
This is good practice to create both structures as they will help you to maintain the project, but if you are creating simple web-application for testing purpose or so, you can directly start with deployment structure.
Thanks
Imran