In a Merkle tree, transaction IDs (txid) are checked to place the incoming transaction at the right location at the bottom of the Merkle tree, and the Merkle path is returned to the SPV for checking the content.
It's easier for the servers to return the Merkle path than to check very transaction to reduce the work-load. Hence, the whole process works out.
The transactions at the bottom are sorted by txid, and the hashed values are calculated for the entire transaction block.