Exactly. In writing you change the question mark to exclamation mark. When spoken, the intonation is rising for the question (with a slight drop at the last syllable), and almost constantly dropping for the exclamation (with a minimal rise on the syllable preceding the last one). This is why punctuation is far more important than in English.
(In English it is not unknown, especially in literature that a declarative sentence ends with question mark to express hesitation or uncertainty. You almost can't do this in Hungarian, but you can express the same indecision with the well formed word order.)
Unfortunately not. "Lent van a fiú" means more precisely "the boy is down there" (in the bottom of the list, down the yard instead of upstairs in his room, etc). The boy is below is not wrong, but a bit misleading for beginners.
For your case, "(Ő/az) a fiú alatt van." is the correct sentence. The -t ending is absolutely wrong in this case, as that means that the boy is the subject of an action. To see the difference, I decided to show you another, very simple sentence.
A fiú kergeti az oroszlánt — The boy chases the lion
A fiút kergeti az oroszlán — The boy is chased by the lion
As you see, the -t is belonging to the person who is chased. In more pro approach, it goes to the subject who is acted to.
- Látja a fiú — The boy sees (him/her/it)
- Látja a fiút – (He/She/It) sees the boy
Megcsókolja a lány a fiút – The girl kisses the boy
Megcsókolja a lányt a fiú – The boy kisses the girl
This is also a good example for the traps of the free word order ;)
By intonation. This intonation (pitch rising till fiú and then dropping) would be very odd for an affirmative sentence, let alone a general one. (In general, since there is no difference for standalone sentences, there is no reason to say "it's sounds more like" one option - apart from intonation.)