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.

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.

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

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