I wake up to use the bathroom often during the night/early morning. I am always confused as to how to wash my hands/which prayers to say. here are some questions: If one wakes in the early morning but plans to go back to sleep, must he say modeh ani both times that he wakes up? if one uses the bathroom in the early morning but plans on going back to sleep, how must he do netilat yadaaim? how must he do it later on when he wakes up for the day?

No need to say Modeh Ani twice. Some say that one doesn't need to wash and say a Bracha, though the Mishna Brura says that it's corect for a Yarei Shamaim (one who fears G-d) to wash and say the Bracha. For how to act later on when waking up for the day see the regular rules in Shulchan Aruch OC 4:2 and Mishna Brura ibid (8-9). Rabbi Chaim Katz