System Settings are always available with a tag and if the tag is in the Template, they will only appear pages that use that Template:
You also have the option of using User Settings or Group Settings, which use the same tag.
Mark Hamstra's ClientConfig might provide a way to set them. If not, you could create a CMP (possibly using MIGX) or just a form on a web page they can visit.
You could do it with TVs, which can be attached to specific Templates, but it would be slower. TVs have a value for each resource, but you could use the default value of the TV. Unfortunately, setting the default value of a TV is not very user-friendly, though again you could create a CMP or form to set them. You might want to hide the TV's from the user in the Create/Edit Resource form, so they couldn't override the default value.