Sometimes you want to create some dinky MSI and don't see the point to go through the SetupCapture route. You should still create a blank WSI and go from there.

NOTE : If you want, you can also create a project entry in the
Workbench but WPS has no "Create from scratch for Windows
Installer" process. YOU have to create the blank WSI file in the
right place in the SharePoint for the links to work right.
Let's say we want to create Widget_V1.MSI to copy a file and plug the registry.
-Launch Wise Package Studio
-Click Tools tab
-Launch Windows Installer Editor

-Select File menu -> New
-Click Ok
-Select File menu -> Save As
-Browse to the SharePoint to the proper folder. (ie Widget_V1)
-Change the name from Untitled.wsi to Widget_V1.WSI
-Click Save
-NOW we have a clean slate.
Now we want to add a file and have it use a "Relative Source Path".
The other
good 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. And
that’s IF you copied the files to the network!
“Relative Source Path”
is used to make it possible to compile the MSI without having to
copy the file(s) to the local PC. If you just browse the C: drive,
find your file(s) and click Add, that file would have to be there,
on the C: drive every time you compile the MSI because WPS adds all
files with an Absolute Path by default. Relative Source Paths solves
this. The problem is that Wise Package Studio does not have an
easy way to add files to a package and use Relative Source Paths in
one shot.
In the SharePoint , under the proper project folder, create the folders and copy the file(s) you need to add the the package. Ie:
Let's say you want the package to install C:\Program Files\widget\widget.exe
you create \Program Files\widget folders in the Sharepoint like this:

Go back to Windows Installer Editor
-In the top window, browse the SharePoint to locate and add widget.exe
-WPS adds the file but creates an absolute source path to the file starting with the [WiseProjectPath] variable. ( This is from Tools menu -> Convert Source Paths)

-Select Tools menu, Change Source Paths

-Click Change Selected Path.. button.
-Change [WiseProjectPath]Widget_V1\Program Files\widget to .\Program Files\widget
NOTE: The .\ is the location for the .WSI file.
-Now add the registry entry that you want. Be it by importing a .reg file or by adding from the PC's own registry.
-Click Compile