Replies in order:
The reason your modifications go away is you are making them in the CSS files (which are rendered per session/cache and/or whenever you change the template settings), however, the CSS core is all in the /less/ folder, If you make changes to the less files, your changes should stay forever.
For the preloader, it's already in the center but the height is limited to 107px and your logo is 207px. please make the following change:
templates/jd_restaurant/less/theme.less Line 1408
JoomDev is not affiliated with or endorsed by Open Source Matters or the Joomla! Project. The Joomla! logo is used under a limited license granted by Open Source Matters the trademark holder in the United States and other countries.