Any ideas as to how I would do this? I have seen that iOS devices can be accessed using WinSCP so I was hoping this would be possible.

It do not think you can achieve that using WinSCP.

I want to do it for a non jailbroken (jailed) device using a .exe program I compile. I just need to know what code from WinSCP to use in order to be able to specify a file path on someones device inside of the Applications folder on the device.

In other words I need to be able to write files to //device_name/applications/angrybirds/documents
That would let me write files to someone's Angry Birds app.

How would I do this as a file path or something that is completely automated so that the files copy with the click of a button?

Not sure what you ask for. Jailbroken iOS device can be accessed via SFTP. WinSCP is an SFTP client. So you can access jailbroken iOS device as any other SFTP server. For uploading files to SFTP server, there are numerous examples here. For instance: https://winscp.net/eng/docs/library#example

I am looking to create a file injector that transfers files to an app directory on click using WinSCP's code for accessing devices running iOS. I haven't been able to find anything about this anywhere online and I came upon WinSCP since it is Open Sourced.

Help?