If I change my DNS settings and use an "Add-on domain", my Mambo installation will go from me.hosting.com/mambo to www.domain.com. How will this affect Mambo + SMF and how do I easily update things that require that?
That depends.
Are you trying to have people access your site with both me.host.com/mambo and also www.domain.com?
You should be aware that Mambo checks the cookie against the variable $mosConfig_live_site for a match. So, if you told Mambo your live site was at me.host.com/mambo when you installed it, it will not read cookies set at www.domain.com.
If you then change the live site info to www.domain.com, the cookies set at me.host.com/mambo will not be read.
So, you can have it one way or the other, but not both.
No, then it would just be through www.domain.com. Is SMF going to cause trouble when switching there?
No, SMF is a little more flexible. Just make sure to change to your new domain in your SMF Server Settings.
Good, thank you.