Learn Portuguese (Portugal): Estás bem agora?

Estás comes from the verb estar, which is used for temporary states, conditions, and locations. Since we are asking how someone is feeling right now (agora), it is a temporary state! You would use és (from the verb ser) for permanent traits.

Where is the word for "you" in this sentence?

In Portuguese, you do not always need to say the subject pronoun (like tu for "you"). Because the verb form estás is only ever used with tu, the "you" is already built right into the verb. Saying Tu estás bem agora? is also correct, but dropping the tu is very common and natural.

Does the word order change because this is a question?

No! In English, we flip the order to ask a question (changing "You are well" to "Are you well?"). In Portuguese, the word order stays exactly the same as a regular statement. You just change your tone of voice to make it sound like a question, and add a question mark at the end in writing.

Could I say "Estás bom agora?" instead?

You should stick with bem (well) when asking how someone is feeling or doing. Bom means "good" and is an adjective used to describe the quality of a noun, like a good book (um bom livro).