If you're hosting the .pac file on a web server which allows server-side includes you can do this.
// Whitelist section from InvisiBill
// Add sites here that should never be matched for ads.
<!--#include virtual="whitelist.js" -->
// To add whitelist domains, simple add a line such as:
// || dnsDomainIs(host, "schooner.com")
// or for a single host
// || (host == "some-host-name")
I use this to maintain a dynamic whitelist and blacklist that I written have bookmarklets for, in conjunction with the noproxy shell script. I can post if there is interest.