not sure yet whether whmap or clientexec.
Might want to check out DRAMS
as well, great system for automation, absolutely fabulous.
You can't just do a "one time" security audit on your servers, this is something that must be done daily, weekly, monthly, hourly, CONSTANTLY. If you don't know anything about linux, find yourself a linux admin and have him or her watch over the box(es). Most will do it for decent rates, and those that are worth their salt will do it not for the $$ but because they love their job, nothing more.
If you plan on running a successful business, you need to either have linux knowledge or hire someone that does, especially with regards to security. There IS no 100% sure fire secured server as long as it's online, but steps can be taken to ensure your server isn't easily taken advantage of