In the manga, Deuce does not dig a grave for a skeleton before meeting Ace.
In the manga, Deuce and Ace find the wreckage of a large ship and use it as material.
Deuce does not discover the fact that Ace is Roger's son.
The manga adds an encounter with a monstrous bird that lives on the island.
The bird tried to devour Deuce, but Ace defeated it. During the fight, the bird spat a chest which is later revealed to contain the Mera Mera no Mi. In the novel, Ace simply found the fruit somewhere on the island.
In the novel, Ace comes up with Deuce's pen name after Deuce threatens to use the name 'Ace'. In the manga, Deuce chooses the name himself after agreeing to join Ace.