1. On the school boat, there were 40 seats for older children in the front and benches for little children at the back.
2. On the school boat, there were 40 seats for older children at the front and benches for little children in the back.
3. In the school boat, there were 40 seats for older children in the front and benches for little children at the back.
(Are they all grammatical? Please check the changed prepositions:in, on, and at. Thank you.)
Since you used "older" in the first part of the sentence, it'd be better if you used "younger" rather than "little" in the second part of the sentence.
"On" is far better than "In" to begin the sentence.
Here's how I'd phrase it all:
On the school boat, there were 40 seats for older children in front and benches for younger children in back.