We're adding documentation for how templates work and providing details of how to create your own as part of tc Server 2.6 which will be released next month. This will include support for a template making a change to a properties file, e.g. logging.properties as is relevant here. However, tc Server 2.6 only support making additive changes to properties files as that's the only requirement that's been raised thus far. This may make it harder, but hopefully not impossible, for you to achieve what you want to do.
For the sake of simplicity, assuming you're on a unix platform, have you considered using a symlink for the logs directory?