Application Cloud File Storage

I've been working on an iOS app recently which will allow users to upload and store documents to our cloud and sync them with their ipads. It's written with a PHP/SQlite backend so far because the database usage has been somewhat minimal, but I've never really worked with storing files securely like this before. Could someone with some experience in this share some insight on the best way I could do this?

My first thought was just to use a MySQL DB to store the files in a BLOB, but I've read that that's a really bad idea performancewise, but rather to store them directly on the cloud site and simply store the filepath in the DB. If I do choose to store them directly on the server, how can I make them non-accessible to anything but my app?

If anyone could shed some light on the best way to approach this, I'd appreciate it!

Thanks! Bryce