I am painfully aware of the risks involved with keeping bitcoins online (https://bitcointalk.org/index.php?topic=255369.msg2749654)... but i i can't trust the exchanges, and I can trust double password access, what is the secure way to store bitcoins onl9ine, specifically with regards to running an online business that moves bitcoins to and fro? 

My original plan was to keep them in blockchain as they seem to have very good security, but as their security was not able to stop my 300 coins for getting disappeared, I guess that is out of the question... so, what IS the best way to store coins online what they HAVE to be stored online?