Yes, it is all controlled with CSS like you mention. Here is what I would recommend. Lets take the Ribbon+Fullsize as an example. The directory that contains the css for the dark and light files is galleries/ribbon_fullsize/css. Copy the dark.css file and rename it anything you want, such as mystyle.css. Now, you can edit the mystyle.css with the colors that better match your site. In the admin, your new style will automatically show up on the Choose Gallery page as a selectable theme under the Ribbon+Fullsize. If you want a custom image to show up as well, you can make a thumbnail in galleries/ribbon_fullsize/admin called mystyle.png.
Using this technique allows you to keep the dark and light themes intact while still creating a custom one that works better for you. If you don't care about keeping those intact, you can of course edit the dark.css directly with the colors you want.