Keystore is used for publishing your Android application APK file, it only has one password and You can change it using keytool, placed in:

c:\\Program Files\\Java\\jre7\\bin\\keytool.exe

to change Keystore main Password:

keytool -storepasswd -keystore your.keystore

Enter keystore password:
New keystore password:
Re-enter new keystore pasword:

to change Keystore alias Passwords:

keytool -keypasswd -keystore your.keystore -alias your-alias-name

Enter keystore password:
Enter key password for <your-alias-name>:
New key password for <your-alias-name>:
Re-enter new key password for <your-alias-name>: