Please bear in mind that we provide the FatFreeCart.com service on a strictly do-it-yourself basis with no support whatsoever (that's a major reason it's free :^), so you're expected to figure it out on your own and troubleshoot any issues you may have with that. If you decide to upgrade to an E-junkie cart subscription (aka "FatFreeCart Pro"), that does of course include support. Since we don't normally provide support for FatFreeCart, we're not actually very familiar with how it works, but we can try to answer your question this time.
Yes, the button codes for FatFreeCart.com are very long, because all product and cart configuration is done by manually editing the button code in your page. You would need to be somewhat experienced in HTML coding practices to accomplish that correctly. The length of the button code itself should have no bearing on your page appearance.
If you decide to subscribe to E-junkie, those cart button codes are much more compact and easier to use than FatFreeCart. This is because you'd perform all account, cart and product configuration for E-junkie via our easy, point'n'click Seller Admin, and all settings are stored securely in our database. E-junkie provides ready-made button codes which you'd simply copy and paste into your site; these button codes just contain a reference to your E-junkie account ID and product ID numbers, which the cart looks up in our database to determine the relevant settings such as price, item name, etc.