A point that puzzles me is how are the miners, following the implied instructions recorded in the blockchain, to manipulate the bitcoins?

Parts of the protocol seem to have the miners sending bitcoins somewhere, or holding bitcoins somewhere, but since the blockchain is the only data upon which to decide which bitcoins to send to where, how are the private keys controlling the bitcoins that are to be moved etc stored?

For example when someone uses bitcoins as collateral and gets a loan, where is the private key of the address used to hold the collateral (those bitcoins) stored?

-MarkM-