How do I compare Ender's game to Hamlet or Life of Pi? How would I format it in a comparative essay? I have 2 topics down but I don't know if...

Your initial thoughts are good for comparing and contrasting those three literature pieces.  The second thought, comparing appearance and reality is the stronger of your two ideas.  Your first idea is confusing to me and, and I'm unclear what "two truths" are being compared between Ender's Game  and Life of Pi. 

I would write the entire comparative essay on the appearance vs. reality concept.  The prompt that you provided said to compare Ender's Game to...

Your initial thoughts are good for comparing and contrasting those three literature pieces.  The second thought, comparing appearance and reality is the stronger of your two ideas.  Your first idea is confusing to me and, and I'm unclear what "two truths" are being compared between Ender's Game  and Life of Pi. 

I would write the entire comparative essay on the appearance vs. reality concept.  The prompt that you provided said to compare Ender's Game to either story, not both. 

You are correct that Valentine Wiggin and Peter Wiggin represent two children who are lying about their knowledge and identity to the world.  That's the same as Hamlet and Claudius lying about their knowledge.  Don't forget that Valentine and Peter are not the only two deceivers in the book though.  Graff is a huge liar.  He doesn't ever tell Ender the whole truth.  Mazer Rackham isn't much better either.  There is absolutely a ton that you could do with your chosen topic and those two literature pieces.  

The second part of your question asked about how to format your essay into a comparative analysis.  That's nice for you, because then you don't have to contrast them.  Only focus on the similarities.  With that in mind, you can set yourself up with a statement/reason thesis statement.  Make a statement, and provide reasons.  For example: "Ender's Game and Hamlet both show the theme of deception through various character lies and the intentional withholding of the truth."  

The above thesis gives you plenty of room to analyze a bunch of different characters and their appearance/reality relationship.  It also lets you talk about plot events too.  Make sure the thesis is the last sentence of your first paragraph.  Be sure that each following paragraph relates back to the thesis.  Use quotes from each novel whenever possible.