By generating a master public key Bifrost is able to derive many public keys / addresses using a single key where users will deposit BTC/ETH. The tool you mentioned will also generate a master private key for you that you can use to derive private keys to corresponding public keys. This is how you can access BTC/ETH deposited by users in account generated using a master public key.
You may also find
bifrost check-keys command useful. It will generate a few addresses using your master public key so you can compare if you get the same addresses (and private keys for them) using other tools.
Any tool that supports BIP-32 can be used to generate master keys so you could even use hardware wallets. When you have access to master private key you can generate
i-th address and private key for this address.
To find which addresses contain funds:
processed_transaction table which contains all transactions that were processed (transactions users submitted to send you money).
address_association table (
address field). This rows will also contain
address_index used to generate private key from master private key (more info in BIP-32).