VSeWSS only deploys to the GAC, and only on the local server. There is
no way to modify most of the settings in the Manifest.xml, Feature.xml,
or elements.xml until after you have completed development. You can
then get the actual files  and modify them to create a deployment project
for production.

This and several other hard coded assumptions are why I don't use
VSeWSS. I just create my own template from a class library instead.
Then I have full control.