Optimising the inputs for a transaction
Every client has different selection criteria based on fees, age of the outputs, and other factors that impact the ultimate fee and priority. Normally older outputs are preferred as they incur less fees. You would probably want the 0.6 BTC output as you'd need 0.0001 BTC for the fee, sending 0.9999 to a new change address. 

There's ultimately no "proper" method as this is wallet functionality and not core protocol.