the bitcoin RPC API documentation is your best friend, it is easy, just setup a script who will be triggered when a user demands an address, basically it will querry the daemon this way : bitcoin-cli getnewaddress [account]
and for coin management, you will have to rely on bitcoin daemon basic implementation, which is : bitcoin-cli move
It is that easy, what i can advise you to do is not to think of it as beign too much complicated, satoshi and the bitcoin dev team made things easy, just make some scripts and test them, remember that you can always find a way to run a .sh script from webservers if needed, or you can do this using the RPC port instead, but you will have to use SSL ports as the data will be exposed, even if it is running in localhost, i advise you to use SSL.