Encrypting passwords
Since you are talking about password-based encryption, the best practice is to use a slow password-based key derivation function to derive the encryption key and only store the salt (and parmeters used). You can verify the correctness of the password by using authenticated encryption, which you should most likely be doing in any case.

The password hash used could be scrypt, or I suppose argon2.

Since you are using this in a password manager -type situation, the encrypted data is passwords, which is fine. The above advice is only about the master password that is used to secure the database. That should not be stored in plaintext or encrypted form and even its hash does not need to be.