Hi CEJM,
The way the software will work means that it will more than likely be "index.php" as the main page.
If you were to create your 'other' section and save it as index.html, then this will appear instead of the index.php in the user's browser where you could go on to link to index.php etc... Another options to put your shopping part into another directory, or "folder", in your public_html directory of your website. From there, you could link to /shop/ etc and have the rest of your website as the first loading page.
Any questions please PM me and I'll try and help you out a bit better!
G'luck