Modules are special. Since you, the theme developer, cannot know what modules will be used by each Form Tools installation, you can hardly be expected to provide templates for each and every one - including those that aren't written yet!
Instead, skinning modules work like so: your job is to develop three special templates: modules_header.tpl, modules_footer.tpl and module_menu.tpl. These three templates do the job of rendering important areas of the module pages for ALL modules, namely: the header HTML, footer HTML and the presentation of the module navigation menu.
The actual job of creating the Smarty templates for each module is left to the module developer. They create whatever pages they need - and they then include the three files appropriately.
The benefits to this approach should be pretty clear: the resulting UI will be largely consistent between the main Form Tools pages and each module. To further reinforce this consistency, the Form Tools core contains a CSS file which should be included in ALL template pages - including your modules_header.tpl file. This lets module developers rely on those rules always being defined. Mostly the file just includes padding, margin and colour rules. See: