There's no extra bonus if you control more than one commander.

Once you've announced that you're casting a spell, players can't take any actions until you've finished doing so. Notably, opponents can't try to remove your commander to change how many modes you may choose.

The commander you control doesn't have to be your commander.

To move a counter from one permanent to another, the counter is removed from the first permanent and put onto the second. Any abilities that care about a counter being removed from or placed on a permanent will apply.

Once you've chosen both modes for the spell, it doesn't matter whether you continue to control a commander. This is true even if you somehow no longer control a commander as you finish casting the spell.