Generic Mod Enabler is a program which allows you to easily install or uninstall multiple game modifications while preserving your original install. After a mod is installed it lets you easily uninstall that mod without disturbing the original install. Making mods support JSGME is very easy, you simply use full paths in the zip file. The tool does the rest. This tool is already pretty standard for use in many other highly modded games like Silent Hunter III and European Air War and I think it would work great for LFS too. It's freeware and I've used it with Silent Hunter III for quite some time with good results.

More details about JSGME can be found here: http://www.users.on.net/~jscones/software/products.html