Theme development and pretty url

hi!

I want to know, if it’s possible, how must i set the url rules for custom posts types and/or his custom taxonomies in a new theme i’m developing.

with WP default options (except the first) for permalinks, i cannot paginate the custom entries listed on a page.

i supose that i must code the rewrite rules for custom types, in a way they will be integrated with the theme, so the final user only need to set his url options as usual in WP, isn’t it?

what would be the way to do so?

Thanks in advice and excuse me if i’m in the wrong section.