site logo won’t display correctly in header

I am working on a new site build with the the Sinatra theme and am having nothing but trouble. I had a really hard time getting the site logo to display at all on my site. Now it displays very small. And on top of that I am unable to make any changes to the custom css. In fact, it seems that all changes that I make in the ‘customize’ section are not reflected on the site. Things appear find in the preview, but none of the pages on my site reflect any custom changes. Is the theme broken, or could there be something else that I am missing?