I am a first time ios developer and cannot find any documentation on private apis. So I have been searching for some type of tutorial on how to use otool. The only certain thing that I can find is that I had to download the command line tools through xcode preferences. I also keep seeing references to linking it to the .app file, but I don't know where I can find this and how to use it in tool. Any links or suggestions?
Here is official documentation
Here is the question about otool usage: how to use otool
How does Apple know you are using private API?
Detecting Private APIs
Here I have a question. Why do you want to detect private apis? Usually, this question happens when you plan to send your app to AppStore. If so, probably iphone-privateapi tag isn't good fit for the question. Since, this tag is more about how to use private api (and implication that the app won't be send to Appstore)
This one is tough. There is no good documentation. Information is scattered and becoming outdate as soon as new version of iOS are released.
Look at these questions to find some interesting links:
iOS Private API Documentation
How to use iPhone SDK Private APIs