lightning network funding transaction clearification
the input of the funding tx is just an input that is able to spend some UTXO which either Bob or alice controlled. Theoretically we could have Inputs from Bob and Alice but I believe that is not being implemented yet. 

The workflow goes as follows. For example alice decides to open a channel by creating a funding tx. The output of the funding tx is a 2-2 multisig P2SH so before broadcasting the funding tx there will be 2 commitment tx created. one for alice and one for bob (in order to be able to ascribe blame in case auf malicious behavior) only if the commitmet tx are successfully signed the funding tx will be broadcasted to the bitcoin network and only if it has enough confirmations the channel will become operational.