Possibilities on future ramifications of formatting formalities

I was studying the phptemplate engine, learning how it works and I was also having an issue with a couple of the modules. I had a thought that needs clarifying.

I was about to go into the modules and mess with the code so that I can format it the way I want and then I thought is it possible to have phptemplate handle this?
Or can we have all modules run there code through a phptemplate hook function?

Does this make sense? I want to customize the html of any or all of the modules pages.

Can the modules be made to pass their html to a php function or have an "edit" tab (created by phptemplate) that allows me to edit the html that is being passed to the page from the module?

I have yet to install phptemplate but I have read almost all of the instructions.