For your branding question:
http://modxcms.com/forums/index.php/topic,41928.msg273647.html#msg273647
Of course you can also make your own manager template and use that, that should be no problem.
Removing all attribution to MODx is a big of an icky subject, you can see that in the tread I linked you also.
Friendly URLs on IIS is also possible. It depends however on your host on how to get it working. There’s plugins like
ISAPI Rewrite,
Ionics Isapie Rewrite Filter (IIRF) and probably much more like that.
The one host I’ve worked with that offered IIS hosting had IIRF rewriting enabled. They also had a check in place for .htaccess files, which rewrites you from your site to their helpdesk explaining how to enable rewriting on their server (using iirf.ini).
To sum it up: if you have full control over your server, check out one of those plugins, else try looking in your provider’s helpdesk or send them a ticket asking what they offer to enable SEO friendly urls using rewrites.