First of all the css-compiled will be overwritten often so you should never be changing anything directly in those files yourself. All custom changes should be done in a custom CSS file or in the template settings (this include the logo).
Next, it's irrelevant what number the layout positions are on when you enter template manager - that is merely a toggle so you can see the different layouts. The actual number of positions is determined by the number of modules you have published to that position area.
The logo on your site appears to be fine? Can you give more details on specifically what is changing (visibly) on your site - perhaps a screenshot.
Regards, Mark.
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