To access the advanced preferences, choose Preferences from Navigator's Edit menu, then click on the word Advanced in the left pane. Clicking on the plus or arrow will expand the Advanced panel, revealing its two sub-panels, Cache and Proxies. Take a deep breath, we're diving in.
Enable AutoInstall tells the browser whether you want it to be able to download and install plug-ins and other updates. AutoInstall does leave you some control -- it won't go installing gadgets without your permission. Call me crazy, but I'd rather be in complete control of downloading and installing software on my machine. I'm no control freak, but if something goes wrong, at least I'll know who to blame.
Cookies are a complicated subject -- everyone has an opinion about whether or not they are hastening the end of life as we know it. Briefly, a cookie is a small message to itself that a web site leaves on your hard disk. The next time you visit a site, it can read the cookie and taylor your visit -- for instance, an art site might remember that you prefer Monet to Van Gogh and act accordingly.
Some Internet users see cookies as a threat to their privacy. So, you can turn them off with the "do not accept cookies" option. If you're more trusting, you can accept all cookies. A healthy medium is "Accept only cookies that get sent back to the originating server" which doesn't allow cookie information to be sent to servers other than the one that put it there in the first place. (After all, you don't want netscapehelp.com to know you prefer Monet to Van Gogh. We'd laugh at you.)
If you accept cookies, you can ask Navigator to warn you before accepting each one. This will become so tedious that you'll surely turn that feature right back off again.
All those settings, and there's still no check box that will prevent web sites from sending and playing those annoying plinky-plunky MIDI songs. Why do I need to hear a techno-Muzak rendition of "A Little Help From My Friends" while visiting your site? I don't.
The Disk Cache setting on the Cache panel allows you to specify how much of your precious disk space Navigator can use for its cache. Somewhere between five and 10 megabytes is fine -- using more reaches a point of diminishing returns very quickly. If you're short on space, it's safe to scrimp, but do try to keep it at least a megabyte or two.
You can change the location that Navigator keeps its cache. I can't think of a good reason to do this unless you have a really fast hard disk on which you would prefer to store the cache. You can also empty out the cache if you feel Navigator's in need of an enema. Eww.
The Windows version also has a Memory Cache setting which specifies how much RAM Navigator will use for the cache. The default of a megabyte is fine for most uses, but it couldn't hurt to bump it up to two megs if you have RAM to spare. There's no Memory Cache setting on the Mac version: to change the amount of RAM the program uses, quit Navigator and go to the Finder. Click the Navigator icon and select Get Info from the File menu, and modify the Preferred Size setting. This number is for Navigator itself and its cache -- whatever the program doesn't need will be used for the cache.
The web is constantly in flux, and the data in your cache can get stale fast. That's why there's the "Document in cache is compared to document on network" setting. This controls how long Navigator should trust the information in the cache. It can verify that the cache data isn't out of date every time you revisit a page (a good choice for obsessive-compulsives. My choice...), just once per Navigator session (a good compromise unless you leave Navigator running for days in a stretch), or Never (not recommended.) If you choose "once per session" or "never", remember that you can force Navigator to update the cache at any time by pressing the Reload button.
The "Direct connection to the Internet" setting is the default for those of us who aren't behind a firewall. Otherwise, you may need to access the web via a proxy: a computer between your machine and the Internet that acts as a gatekeeper for data. Choose Manual proxy configuration or Automatic proxy configuration, depending on the whims of your friendly network administrator. Enter the settings that he says to use. Wait until the holidays, then give him a nice big present to ensure he stays friendly.