If you put them elsewhere, before running the compare, click the Display tab, click Browse next to Input directory, and then select the folder where you put them.
These are the main files System Architect Compare uses to create a comparison website:
panel.css
This stylesheet is referenced by the XSL stylesheet, and by the HTML files. It contains settings such as font size and color, heading sizes, hyperlink colors, table headers, and so on.
default.htm
This is the main page for your comparison website. It sets the layout of your comparison results, which is comprised of four framesets, one for each of these files: footer.htm, header.htm, main.htm, browser.htm.
embed.xsl
Contains style settings for the information displayed in main.htm. This is the default page that the comparison website opens in, and it shows the server, databases, output file and compare by values that were used to create the comparison. The file references panel.css, but also applies its own settings.