The resources you see are being inserted by the wr:LinkedResources generation tag, which is present in all default Page templates.
The only option available is not to use the wr:LinkedResources generation tag.
- Generate your JSP once with
wr:LinkedResources.
- Copy the block of generated
script and link tags from the created JSP into a custom Page Template.
- Modify the resources as needed, respecting the original order.
EDIT
If you want to dynamically manage resources depending on which templates are being used in the page, a solution is using the wr:LinkResource tag, which is available in the latest WebRatio 6.1.3 release. Basically, you state which resources a template needs directly at the template level (unit, attribute, etc.) and the main wr:LinkedResources tag at page level collects and prints all needed resources.
More information is available in the WebRatio integrated help.