You can remove the images once you have added them to your gallery, the gallery will keep them stored for you.
As for the include file you just need to ensure that the links to this file have the correct path on the end page. So if you add the code for the include without any subdirectory specified and the pages that the content is supposed to display on are in the root of the site then it should work out. Just think of it like you were adding that code directly to the page rather than through the CMS.