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I cannot find way to generate the APK file by using JKS or PEM files in the Visual Studio. If you cannot find the .keystore files that generate by VS, you can find it by following path.(The AppData folder is hidden by default and you may need to unhide it to access it.)
The resulting keystore resides in the following location: C:\Users\USERNAME\AppData\Local\Xamarin\Mono for Android\Keystore\ALIAS\ALIAS.keystore For example, using chimp as the alias, the above steps would create a new signing key in the following location: C:\Users\USERNAME\AppData\Local\Xamarin\Mono for Android\Keystore\chimp\chimp.keystore
Here is a article about it.
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