Though I haven't worked with print module but as per Drupal structure, if you have to override any CSS file(in your case print.css) of some module, you can simply write your style in your own CSS file which stay in your theme directory. But if you want to use the same file & keep your styling separate then simply cut that from the module directory & paste in your theme directory...mention the CSS file in your INFO of theme...and extend it as much as you want...
Don't forget to clear your cache after you do cut/paste & done with INFO file edit..
In same way...you can copy your print.tpl.php file from the module folder & paste in your theme directory(no need to mention tpl in INFO file)...& then you can do as much editing as you want to have custom look...clear your cache in this case too..
I hope this will solve your worry about maintenance as you will get this file in your theme folder itself...