It seems that the “dark version” setting is overriding any css parameters used in the Theme Options. For example, anything selected in Theme Options for content background image/color, input color/background, etc gets overwritten by the dark.css file
We have checked our test installation and don’t see described problem http://prntscr.com/gpcyu1
Could you provide me the link to your site and send either temporary access to your Dashboard or screenshot of Theme Options at least.
Input color for the search we’ll fix in next theme update.
To change the color of the background you need to change the color of the container http://prntscr.com/gpj5w0 if you are using wide version, in other case it will use default color from dark.css or style.css. Side bg is visible when you choose boxed version, wide version has 100% of container that overlaps the site bg.