I have designed a web and mobile application process that has 2 different functions and processes working on the same application. I have discovered through patent search that they both seem to be unique. I would like to protect both applications from being copied. They perform 2 separate tasks and functions but they both function off the same information required. I need to know if i should patent as one invention or should I patent separately? I also need to know that if I patent the whole application as one invention, someone can or will copy just one of the 2 functions as an application because i have combined the invention?
You can try to combine them into one patent but the patent authority may not allow you to. If you do, you should have separate claims covering each function. As long as there are separate claims, no one should be able to circumvent by just copying one function or the other. That said, the patent examiner very well might make you split up the two inventions into separate patents. This happened to me. I invented an algorithm for analyzing PCR reactions. The algorithm generated two separate values which provided different information about the reaction. We had claims for the use of value "A", value "B" and the combination of "A" and "B". The USPTO made us split this into three patents. The international patent was granted as written.
I should also caution you that not finding your idea in patents doesn't mean there isn't other prior art. Especially with software, there are significant sources of non-patent literature any of which could impact patentability. Now, the patent examiner might not find it either, but that is a different issue.