My approach is to create a "GLOBAL" template, well that's what I called it anyway, containing the following:
[[includeFile?&phpfile=[*templatePath*]/template/template.php]]
Within a document I have a template variable called templatePath that I've setup with @INHERIT as the default property. I then set each master folder or documents "templatePath" TV to something like "assets/issues/march" or whatever you want to call it.
In the file system I have "assets/issues/march/template/template.php" and sub-folders containing all my css and images. Within the php template I use the TV value for linking to stylesheets and images, and in certain cases have found that I need to set a php path variable as well.
Not sure how complicated your setup is going to be but I've found this works really well for me. You see I'm doing a monthly ezine and each issue has a different feel so managing multiple templates with the Manager was a nightmare, with this approach I use a single template and change the path to what it includes - sweet - no more stressing!!!
If you need some more help please don't hesitate to ask.