Foundation comes in two flavors for css and js includes. The unminimized versions of each js file can be used separately, or you can use the minimized versions. The single files are simply shown/used for development purposes. If you want to only use some, then you'll want to minimize the js yourself and only include the ones you intend to use.
Alternately, the minimized css for foundation can simply be called up, and you would override that as needed in your own stylesheet.
You may also be interested in pulling Foundation from a CDN.
http://cdnjs.com/ has nearly everything available out there with versioning even, including Foundation, jQuery, and modernizer.
An additional tool would be the MODX Extra, ClientConfig.
http://modx.com/extras/package/clientconfig
With ClientConfig, you can include the scripts from the components menu in the manager, and update them as needed rather easily.