If you want to reuse customized stylesheets and javascript files in several templates this is only doable by a dirty hack.
The hack
Create a new template. Do not add it to any to any Template Type Context.
Put whatever css or javascript you want to add to the file.
Do not use the $ sign (or if so, encode it). However, if you do use the $ sign it will most likely work anyway.
## Obtain the template manager
#set($templateManager = $timeTrackingComponentManager.getTemplateManager())
#set($templateCss = $ $templateManager.getTemplateByKey("mycsstemplate"))
<style type="text/css">
$!templateCss.getVelocityFileObject().getContentAsString()
</style>
You can do the same with JavaScript.
Or if you only need css or script in one template file, just add it directly to velocity template file.