I also need to understand that how safe are wallet like Atomic Wallet and exodus~
If you are seeking a non-custodial wallet, using Atomic wallet and Exodus is the last thing you want to do. Both wallets are closed-source with that it should raise the doubt if you are truly seeking a good one.
~Atomic wallet is secured by a mnemonic key but if I use eth, trx or any other coin address with it, where are where are their keys ? Are they stored in wallet and Atomic wallet key are acting as "master key" for all ?
What if I want to manage ETH separately, how will I do that ?
Yes, to simplify, the mnemonic key/seed phrase is the master key of all of your cryptocurrencies. All the cryptocurrencies private keys are derived from your mnemonic key.
If you want to use a separate ETH address, you can simply generate a new address, the new address will simply be generated based on the mnemonic and the wallet itself will do the job in the back end.