The cockpit

InIn the dim, swaying light of a single lantern Stephen saw someone looking at him with a mix of respect and anticipation. “This is Jamie, your loblolly boy, said Jack, (“though to be sure, she is loblolly girl, or even a woman,” thought Stephen) and this would be your station in combat.”
InJamie stepped aside and Stephen saw a group of wooden chests that had been lashed together into a low table. The room, and the chests, were painted a uniform red. “This would be the operating table, I take it. But is it not strangely dark and damp? Relatively speaking, that is – I mean no reflection upon your ship, upon my word.”
InThe Sophie, of course, was a sloop, not a ship, and though Jack might have excused its being taken for a brig (indeed, its general outline was very much that of a brig), his first impulse was to correct Stephen’s mislabeling of his command. “But,” he thought, “he is a guest, and he may not be used to the ways of the sea yet. And I hope that he will stay and agree to be our surgeon, which may not happen if I am constantly critical,” so instead he only said, “well, yes, we are under the waterline, you know. You’re much less likely to have a cannonball interrupt your work down here than if you were up above, and it will be a bit quieter, too.”
In “Is it very loud during a battle?”
In “Oh, yes, particularly when you’re right next to the guns. Even four-pounders like ours make a tremendous din when they are fired, and if we can get some long twelves, they make even more. I remember that after the Nile, a particularly furious fight, we all had to talk in a roar for days afterward. The guns had been so loud that it affected our hearing, do you see?” he added, when Stephen made no reply.
In “I believe I understand,” said Stephen. He had advanced into the room and was peering into its darker corners. “I don’t see any instruments here.”
In “No sir,” said the loblolly boy, speaking for the first time, “no sir, Mr Blankney, the former surgeon, he took his instruments with him and we have yet to receive a new set.”
In “Ah,” said Stephen.
In “The Sick and Hurt Board sends a chest aboard, or so I have heard.” Jack said. “Come, let us go up on deck again. I’ll show you the masts and rigging. Jamie, see that we get some instruments from the Sick and Hurt, or do you think that you’ll need Dr Maturin to accompany you?”
In “Begging pardon, sir, but I don’t know. I can check and let you know, if you would like.”
InJack nodded. “Yes, do that. Dr Maturin, after you. We’ll go up the ladder to your right.”

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I'm not sure that the first paragraph works, whether it's clear enough that Stephen's thoughts regarding the loblolly boy run concurrent to Jacks speech. It might be too muddy. Thoughts?