I’d rather just upload a header image with the customized dimensions, but overtime I upload the image it doesn’t appear on the site. Not sure why that’s happening?
Did you get this sorted out? I see no duplicated logo, and I see your custom header displaying:
http://tappinginfinitepotential.com/wp-content/uploads/2015/07/cropped-Header2.jpg
Thanks Kathryn, yes I just edited it in the CSS editor. Any idea how to get rid of the gap between the nav bar and the header?
Did you edit the theme files directly? There shouldn’t be a gap there using the theme’s custom header feature, as you can see in this screenshot:

If you edited the theme files directly, all your changes will be overwritten whenever the theme is updated.
I’d suggest you use the theme’s built-in custom header, or a child theme, so your tweaks won’t be overwritten when updating the theme. Here are some guides in case you haven’t made one before:
http://codex.ww.wp.xz.cn/Child_Themes
http://op111.net/53/
http://vimeo.com/39023468
If you go the child theme route, be sure to add a class on your image so you can then target it with CSS to change things like padding and margin.