As long as our web crawler can access the page content of your intranet we will be able to index it. Currently, there is no way to add login/password credentials directly to your crawler settings for protected pages. However, if you are able to configure your server to open access to our crawler, we are able to provide you with an account specific user agent string.
Another option is to use our developer API to index your content. That way you're in full control of generating your search engine and result documents.
We recommend using SSL to transfer your content securely between your intranet and our servers.