You're are misundersting the keystore :
- The keystore is a file which identify you (to securize your release), don't name it *.apk, it's not your application build
- You can store as many key in your keystore, one for each application you want to sign with
So you just have to create a first key on your keystore by providing an alias and a password
Then you'll have 1 password for opening your keystore and one for signing with the desired key (alias)