Hi Lars,
In building the links in your module control I would not hard code the site folder in the path like:
~/customfolder/custompage.aspx
where customfolder is the site folder. That would break it in the root site if you code it that way.
If your module inherits from SiteModuleControl there is a built in property for SiteRoot that will include the folder name as needed, so you build your link like
SiteRoot + "/custompage.aspx" (I would also pass in the pageid and module id as query string parameters).
If your module control is just a plain usercontrol then you can do:
string SiteRoot = SiteUtils.GetNavigationSiteRoot();
then use it to build your url the same as above.
You could find examples of how links are built by studying the code of other mojoPortal features. Really for any troubles you may have in custom feature development, you can find something similar in existing features to get ideas how to do things.
Hope that helps,
Joe