a classifieds system / directory listing that ties in seamlessly through use of WP native functions
If your theme was written according to regular WP conventions it should look fine. See http://classyfrieds.com for a random selection of themes through our theme-switcher. However, we do get a lot of requests for commercial theme support. Some of these themes use custom headers or redirects which may hamper or even break classyfrieds. We do offer theme support through our commercial freelance activities.
categories in classyfrieds are separated from normal categories so they will not show in your regular post-category sections and are contained to the classifieds. Tags on the other hand are purposely mixed with your regular blog tags, so if you run a tag-cloud or other tag widget it will also show tags from your directory listings or classifieds section.
We don't know ! We'll need some more information. Drop a line in our forums and be specific about your problem. In the meantime, try visiting the permalink settings in your admin panel, and read the first-light section inside the plugin admin UI.
The forum over at http://classyfrieds.com/questions/ is monitored most frequently by the developers. Alternatively you could try and post on the plugin page at wordpress.org but be warned that we do not visit those forums regularly.
At this time it appears the following plugins do not play nice with classyfrieds: * bbPress Antispam version 0.7 (pre-mature version) * Some IE layout issues may present itself on some themes. I will attempt to keep IE compatibility going as long as I can.