I know Simple XOOPS is supposed to be integrated into XOOPS at some point, along with SEO friendly URL support.

The thing is, I want to make sure this will be supported in my future modules, so what is the best way of building and presenting URLs?

By that, I mean - either build the URL in the code and send a variable like "$url" through to the template, or send the individual parts to the template and put it together there? I suspect the former, but having no idea how this will be implemented, I would just try and save myself hassle later on.

Either is OK.
URL assembly will be available both at controller layer (for say a PHP file) and view layer (for say a template file)