I really hope you don't have to deal with this. I'll keep this short as I can, but some of you are probably going to have to deal with some interface of one kind or another.

The Yahoo! Store is an interface. If you are stuck with this you probably won't be very effective at optimizing your site. It's already predetermined that you can't access all the code of the site.

Interfaces are software, generally a web page like a Control Panel, that is the only way to upload or download files. If you are allowed to upload and download, you are at least part way ahead of the game. It won't be as easy as doing it with FTP, but you'll at least be able to control the code inside of your pages. The basic interface will provide you with input boxes to type your content into, but the code controlling that content will not be accessible.

ShopSite, Yahoo! Store, EasyEdit, ... oh, I'm brain dead right now. There are quite a few well known names out there that do not allow you to access and edit the code, and generate it for you.

My advice is to steer clear of this type of setup. If your hosting company says this is how you have to do it, Google for another webhosting company.