If the same mode is chosen more than once, you choose their relative order as you cast the spell. For example, if you choose the second mode of Eldrazi Confluence more than once, you choose the relative order to exile and return the target nonland permanents.
If a mode requires a target, you can select that mode only if there's a legal target available. Ignore the targeting requirements for modes you don't choose. Each time you select that mode, you can choose a different target, or you can choose the same target.
You choose the modes as you cast the spell. Once modes are chosen, they can't be changed.
Magic: The Gathering · ™ & © Wizards of the Coast · Illus. Hristo D. Chukov
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No matter which combination of modes you choose, you always follow the instructions in the order they are written.
If all targets for the chosen modes become illegal before a Confluence resolves, the spell will be countered and none of its effects will happen. If at least one target is still legal, the spell will resolve but will have no effect on any illegal targets.
If a Confluence is copied, the effect that creates the copy will usually allow you to choose new targets, but you can't choose new modes.
No player can cast spells or activate abilities in between the modes of a resolving spell. Any abilities that trigger won't be put onto the stack until a spell is done resolving.
