What while the clerk say?
 

When I am in a 7-11, how will the clerk ask me if I want to heat my items up in the microwave?

温めますか？
Atatame masuka?

The microwaves are on a counter near the exit, so you just go to the counter and help yourself. They will gesture to them if they don't speak English.

They arent always on the way out. The one closest to me has them behind the counter and they ask if you want it heated. The first post is usually what they say. I have also had them ask me if I wanted to eat it now.

食べましょうか。 Or something similar to that.

Sometimes they also ask you if you need chopsticks or not.

Yeah, I've been in countless convenience stores and I've never seen self service microwaves. They'll say what SumireSato said.

Hot food!
 

Excellent, thank you!

When referring to chopsticks, would a Japanese clerk typically say "O-hashi?" or "hashi?", or refer to them as "waribashi" (disposable chopsticks?)?

Also, Anything else I need to know about convenience store etiquette? While I plan on going to restaurants, I also plan on many meals at my hotel's 7-11!

ThrenodyT

And how do I say..
 

"No, thank you!"? I remember vaguely a term that involves "chotto" but that is all.

How do I decline something gracefully in Japanese?

Threnody T

I think I usually hear お箸おつけしますか？ (ohashi otsukeshimasuka?)
To decline you can say 結構です。　(kekkou desu). I think いいえ、大丈夫です (iie, daijoubu desu) is okay as well.

Supermarkets usually have self-service microwaves but I never see them in convenience stores.

If you know both words, does it matter? You're going to waste brain resources (and make it more likely you'll psyche yourself out and fail) trying to just "prepare" for every conceivable word combination.