Learn Portuguese (Portugal): A rapariga é de Londres?

In Portuguese, yes/no questions use the exact same word order as regular statements (Subject + Verb + Object). You don't need to move the verb to the front or add a helper word like "does". A rapariga é de Londres as a statement means "The girl is from London", and simply adding a question mark makes it a question.

How do I make it sound like a question when speaking if the words stay in the same order?

Your voice does all the work! To turn a declarative sentence into a yes/no question, you just raise the pitch of your voice at the very end of the sentence. For this sentence, your voice should go up on the word Londres.

I learned the word "menina" for girl. Can I use that instead of "rapariga"?

You can, but they imply slightly different ages. A menina is usually a young female child, while a rapariga is typically a teenager or a young woman. A quick warning: rapariga is a perfectly normal, everyday word in Portugal, but it is considered offensive in Brazil, where they use garota instead!

Why do we use "é" (from the verb "ser") here instead of "está"?

We use ser because being from a certain city is a permanent fact about someone's origin. In Portuguese, you use ser for permanent traits and origins, and estar for temporary locations or feelings. If you wanted to ask if she is currently visiting London, you would use está.