Here is what I do. For cold storage it is really simple. I keep copies of the public and private keys and send coins to the public address. I don't need to worry about any software until it is time to spend the coins, which I have never done to date.
Even then you won't necessarily have to worry about the keys! You could just sign your transactions on an offline device that's never connected to the internet and then publish the transaction on your main machine. That way no one can ever get hold of your private keys!