If these instructions don't help consider the following but when don't just try this first solution, read through the article.
Take a look at the following Microsoft Installer project in place of ClickOnce. You set the path e.g. C:\Program Files (x86)\PayneSoftware\SomeApplication.
There is documentation to read before trying.
We used this installer with signing and a local SQL-Server database.
Can't speak about app.config with settings done conventionally, ours are done using appSetting section and after four years never had a need to add or remove settings.
We use VeriSign for signing.
So the above is an alternative to ClickOnce.