The files that compose our Intranet are randomly stored among a few different servers. They are all IBM AIX. When Webinator indexes the site, will it only do one server or will it index across the different servers getting the whole site?
Webinator only walks URLs it is specifically given, or that are links from pages it has walked. You'll either have to give URLs to those servers to Webinator (eg. on the command line), or make sure they're linked from page(s) that Webinator is walking.