To use a design you have as HTML and CSS, put it into a clone of an existing skin. The skin already handles logins, profiles, lists and the ACP; you change how it looks.
header.tpl, and its footer into footer.tpl. Keep the Smarty tags of the original templates that load the skin's CSS and JavaScript and show the menu.index.tpl, and replace its sample content with lists made by {jrCore_list}.css/ folder, and register it in the skin's include.php (see below).img/, and show them with {jrCore_image image="name.png"}.Work through the other templates, such as profile pages and item lists, the same way.
Add a line like the skin's own ones to include.php, in the skin's xxMySkin_skin_init() function:
jrCore_register_module_feature('jrCore', 'css', 'xxMySkin', 'mydesign.css');