How do you manage a product based on Linux?

Ryan writes: "My company, following my advice, has decided to base it's new appliance on Linux. So far, it's worked out great. Linux gave us a huge jumpstart on development because of it's open nature and public mailing lists. We've added software, modified startup files, and build our own kernel. Now the question is: How do you manage all that? Do you put it all in CVS or Subversion? Do you use the distro's packaging system(we're using Debian)? What does your build system look like? I'd like to hear from anyone who has worked on a project like this before."