OK - I know how to export to HTML5 and FTP the files to my site, that works fine and I've done it on a few games.
When I do that, the game basically takes up the whole window, even when I have it 640x480, I want to make it more like the game is embedded within my website with my other menu and sidebars on my site.
OK nevermind, I found out how, use the iFrame, I found a tutorial here that explains it:
Develop games in your browser. Powerful, performant & highly capable.
You can add any flash games onlinegame7 to your own website. Just click on a game, copy the HTML code below and paste it into your site.