Right now the admin isn't covered by the template overrides, so anything you change in an admin file will have to be changed again when you do an update. Get something like WinMerge or BeyondCompare to help you compare the new (upgrade) files against the files you changed. It'll make life easier.

Changes to the admin like you just mentioned won't be touched during an upgrade. If you don't want coupons, you won't have them.

For template overrides, anywhere you see a "classic" folder, you can create a folder for your template. Only copy the files you need to change into your template folders to keep upgrading simple. WinMerge or BeyondCompare can help with that too.

To create a very basic custom template (you can build from there), you need:
includes\languages\YOUR_TEMPLATE\english.php
includes\templates\YOUR_TEMPLATE\template_info.php
includes\templates\YOUR_TEMPLATE\common\tpl_header.php
includes\templates\YOUR_TEMPLATE\images\logo.gif
includes\templates\YOUR_TEMPLATE\css\stylesheet.c ss