If I understand your problem correctly then I think you're mixing concerns. It sounds like you have an install that requires admin privileges. Therefore to install the application an administrator runs it for the user. This is assuming the user isn't an admin and UAC is enabled. In this situation the "logged in user" is the administrator. They are running the process in an isolated login session and none of the other login sessions are relevant. Thus the administrator's AppData directory is the logged in user's AppData.
In the other scenario where the user is an admin and they get elevated via UAC when running the installer then the user (and their elevated user account) are the same and therefore the AppData directories are the same. There should be no issues here.
Now comes the question of why your app needs access to the AppData directory. There are a couple of situations that come to mind. But one very important thing to consider here is that the user who is "logged in" when the app is installed may not be the same user that runs the app. Of course your installer could be per-user but in that case you wouldn't need an "admin" account to install it so I'm ignoring that situation.
- Your installer needs to drop some "starter" files such that when a user runs your app they can access the files. In this case it makes the most sense to put the starter files either in the application's directory itself or perhaps in the common appdata directory. This gives all users access to the file(s) and at app startup you would want to detect that the currently running user doesn't have a copy of these file(s) in their own appdata and therefore should be copied over. I would argue this is the most common case.
- Your installer needs some data files that are shared by all users. In that case the data needs to reside in a shared location and the common appdata directory makes most sense.
- You want to write data while your app runs. In this case it isn't an installer issue but something your app would do at runtime. At runtime you would have write access to the currently running user's appdata directory and can store files there directly.