Can I upload html files using FTP or make changes to the cart using my own files?
No. The cart has many automated/dynamic features which are embedded in the source code. All changes you make can only be done via the cart admin which can be accessed at http://www.myshopkart.net/your_store_name/user/ . But you can use an html editor to design changes then copy & paste the html into the edit html sections of the admin.