I find modules migration allways a bit more tricky. Custom (HTML) modules and menu modules will go fine, but on the Joomla 1.5 website I have also used a lot of Display News modules. And these can't be migrated automatically. I will do these by hand. So in order to prevent these modules to come into the 2.5 website I will remove these first and remove all unpublished modules as well.
There one other complicating thing here. I allways manage modules the NoNumber's Advanced Module Manager. So I will have to migrate these settings too. But that will come later.