We are looking to create a similar document to this one with comments that pop up when you hover over them and in a nice design like this website. How did they host it in this way? I can't get mine to look anything similar to this set up
With Acrobat you can mimic such effect. It's a multiple step process.
1. Use the comment tools to highlight the desired text portions.
2. Then print this form with the Adobe PDF printer to create a new PDF which contains the highlightings. You'll have to activate this in the print dialog.
3. In the newly created PDF use the form tools to add button over the highlighted portions. Set their fill and border color to none and add the Tooltip to be displayed when hovering over the button.