Question is: How do you manage hundreds of addresses and where do you store securely your keys without relying on 3rd party wallets, like coinbase?
For security, it's best not to store the bulk of your Bitcoins online. Ideally, they shouldn't be stored in a local client on an Internet-connected PC either. A good approach is to use a local client such as MultiBit (
https://multibit.org/) or Electrum (
http://electrum.org) for your "spending money," and an offline wallet for any Bitcoins you aren't actively using.
I have a few articles that walk through this in more detail. If you're interested, the best place to start is here:
http://www.bit-buddy.com/bitcoin-wallet.html.