How to update apps without using the App Store?

I downloaded some apps off of the Internet and transferred it to my IPhone 4S using a program I have on my computer called ifunbox. Anyways, when I tried to update apps using the App Store it said You have not owned the major version of the software. But it didn't say that before and I don't want to delete my free apps of course. But I was wondering if there was an app, program, or a Cydia source that would let me update my free apps. And whoever answers this question really good I'll give your answer five stars and choose it as best answer.

Umm are you pirating apps?