In the Wise Package Studio (WPS) Workbench you have 2 tabs: Projects and Tools.
Using Projects is the preferred method because it types in fields automatically for you, creates WSI files with “Relative File Paths” and copies the source files to the Share Point. With “Relative File Paths” you don’t need to install the package just to do small change and compile a new MSI. The other bonus about using “Relative Source Paths” is that if you move the contents of project folder or rename the project folder, you'll will still be able to compile the MSI. If you stay with the default Absolute Source Path, you'll have to go to Change Source Paths in the tools menu to change the Source Paths. Also, if you consistently (and properly) use projects, others people can check to see how one package or another is progressing.
The only catch with Relative File paths is when you need to add files. Even if you add them in the proper folder in the Share Point, WPS is not smart enough to notice that the rest of the package is using relative file paths. YOU must fix that manually.
Either way, I will show you how to use Wise Package Studio with and without Projects.