I am not sure what was your deal with the company, but they are definitely not creating a custom application for you.
OS Commerce (
http://www.oscommerce.com/) is ready, open source package. It means that they do not pay anything for it and using ready product to set up your store. With a bit of time and patience you would be able to do it on your own without any programming knowledge.
I don't want to comment on OS Commerce features, but in my opinion, the over all result is not very nice looking and you will not be able to have a custom store application.
You should really go back to the agreement with the developer and point that this is not a custom build store and if you indeed accept using OS Commerce, then you should re-negotiate your contract.