I chose the 1st class template because I liked the how the main image took over the top of the page and the main content area fell below it. On my version, after installing the wigetkit slideshow, the image is in the same place but the main content area totally overlaps it. I've checked the documentation, I checked the forum. I couldn't find anything that addresses this. I feel like I am missing something really basic...

A logo must be placed into the "logo position.
After that you can se the "margin" at the template parameter.

demo.joomlaplates.com/jp_ultimate/docs/#4
You can set the height of the header where the logo is stored. If you dont want any gap between logo and header set the margin to 0px. If you want a gap of 10px between logo and header set the margin to: 10px 0.