The issue with the template is really just a limitation to the way templates work.
When using templates, you can either apply all your server behaviors to the template, or you can apply server behaviors to the individual pages.
Obviously, applying the server behaviors to the individual templates is more desirable.
This is where framework builder and themes comes in handy. Using framework builder themes themes allows you to over come this inherent limitation to dreamweaver templates.
In the Videos tab of the Design Extender support page there is a tutorial "How to convert your site from DWT-dependent to theme-based" that talks about converting templates to themes:
For the file field validation issue, there is probably Spry Validation and Server Side validation applied, you will need to remove the required validation from both.
for the issue you are having editing the upload behavior, see this post: