Hello there, @lbethany ...
It looks like you are in the right area to change all those hex values to what you want so that it matches your school colors / the official hex colors that have been chosen by your school's marketing department. When you change those values, you only see a preview of what things will look like on the right side of the screen. Nothing has actually changed yet in your Canvas environment...which is what I think you may be having difficulties with. If you take a look at this Guide:
How do I create a theme for an account using the T... - Instructure Community (canvaslms.com)
...go almost to the very bottom of that Guide and look for the heading "Preview Theme". You'll want to click on this button to preview what your theme will look like. Then, you'll want to click on the "Save theme" button to save it as a theme you've created on the admin side of your Canvas environment. Then, finally click on the "Apply theme" button which will apply the theme across your Canvas environment. So, it's a few button clicks...and I'm guessing that you just didn't do all of that.
When I was in higher ed, I configured our environment to match our school colors as well. I changed the Canvas logo in the upper left corner to our school logo. I don't recall what the dimensions of that image were, but I do remember it was a square image...because there was a solid color from the theme that you could see behind the image. Maybe you'll just have to play around with a large logo and scale it down in a graphics editing program before you try uploading it to your theme.
I'm not quite sure how to answer your last question...but maybe someone else might be able to chime in on that one.
Hope this information helps in some way!