This is sad, but my main question is: what does checking "Primary" do? I've found more than enough information on installing and troubleshooting the "WordPress MU Domain Mapping" plugin, but basically nothing about actually using the basic plugin features. I'm sure it won't be a problem to do the rest, but I am surprised I haven't been able to find a post that just goes through the basic steps and option when mapping a domain. For example: why would it matter what the "Site ID" is?
One more question as long as I'm on here; how do you go about adding the "www." prefix to the main domain (and mapped domains for that matter)? The update says that the new version of the plugin supports it, but so far I haven't seen that option (for the main site at least).