Sorry for the late reply. This is from the home page:
The folder structure that WSPBuilder uses to build the wsp file is actually the same folder
stucture you will find in: "%Program Files%\Common Files\Microsoft Shared\web server extensions\12"
So all that you have to do, is the create a \12 folder in your project and add your files to
that folder matching the same structure as if you where to put them directly into the
"%Program Files%\Common Files\Microsoft Shared\web server extensions\12" folder manually.
So using this info i created the structure i wanted in my project (features etc...)and then build the WSP file using the WSP builder. This created the WSP File and it contained the libraries and all the xml needed. Then i copied it over
to the sharepoint server and then deployed the solution via stsadm.
I'm not entirely sure if this worked but when i created just the feature folder structure WSP Builder build a WSP file as a Feature and i could deploy just a feature using stsadm, but i am not 100% sure this worked, i only realy deploy solutions.