I'm wanting to know the best practice for deploying this with the function app in regards to having multiple functions deployed to the function app.
This is an interesting question and is based on a couple of things. I would suggest reading this: Function organization best practices.
At the moment I may have to have one instance of this project deployed to the function app per project I am wanting to integrate, I'll be using a timing trigger but I would like to know if this is the best way to solve my integration issues.
I am sorry, I am kind of lost here, does that mean you need to have multiple timer trigger functions in a single function app and you need to know whether it's alright? If that's your question, I see no issue with that.