The index file you need to edit is contained in the theme folder. To get there click on the option in the modeller project and open deployment directory. Once in the deployment directory you will see the theme folder. In the theme folder there will either be a index.html or a zip file for your theme. If you have a zip file, unzip it and edit the index.html and then zip it back up, then replace your old zip file. If there is no zip file then simply edit the index.html, save it and then redeploy. You may need to also clear your cache.