Not dumb questions at all. One, in fact (the saboteur positions) has multiple answers.
So to answer as best I can:
---------------------
The saboteurs can be in a variety of places, depending on when the party arrives. Check page 15 for the steps of the sabotage.
- If the party finds them VERY early (as in, probably before the duchess even goes off for her nap) (they won't, unless they have some super-clever plan), then the saboteurs will still be rigging the alarms. Again, this will likely not be the case.
- If the party finds the saboteurs and the saboteurs have received warning that they have been found out (say, Sokana fled from the party, and the PCs were a few rounds behind her because they stopped to deal with the halfling assassin), then they'll probably be by the relief valves, closing them as the party enters the room.
- Otherwise, if they didn't receive ample warning, they will likely be minding the boiler, putting on occasional shovelfulls of firegems
In my fight, the engineers started in front of the furnace, as the party came down the ladder beside the smokestacks, and had to try to run past the group to get to the valves.
---------------------
There are a few ways to get between the decks, though the ladders are the main one. The staircase doesn't reach the bottom deck, so that's out, but at the front and back of the ship are black squares. Those are openings for cranes to lift cargo through. If the party wanted to open those, they'd have a quick (but dangerous) fall between decks. But yeah, the ladders are the standard way. Keep in mind all three sets of ladders, though.
---------------------
My assumption for the firegems is that, when opened, the gems scatter around the deck in a thin layer (not enough to make difficult terrain), and pour out with a decent amount of force (so they travel a fair distance across the deck). The furnace blocks this motion, so they pile up there. Think of how snowbanks form when wind pushes snow against a solid object, except this is just kinetic motion instead of wind.
That said, I'd rule that the three squares beside the bin are difficult terrain as well. Because physics. But yes, the level of firegems will be larger at both the start and end of their falling path, so they can pile up beside the furnace, too.
So I'd make 9 squares of difficult terrain. 6 beside the furnace (3 across, by 2 out from the furnace) and 3 beside the bin. Those three don't really matter, though.
---------------------
The gems are not hot.
Yet.
Firegems, if you look in the player's guide, are basically alchemical coal. They don't come burning, and are very stable. That said, the ones piled against the furnace (as in the three squares directly adjacent to the furnace) are there to heat the furnace up further, which means they're insulating it, and therefore are subject to heat themselves.
I'd say that after a couple rounds, they begin to heat up, acting like the ones that get shoveled out of the boiler, but only dealing 1 damage to people in their square.
A couple rounds later, increase it to 2. Then 3, 4, and stop at 5, the same as the gems shoveled out of the furnace.
Once they hit 5, I'd say they're not hot enough to heat up the piles next to them as well (the other 3 from the 6 squares of difficult terrain that got spilled). Again, start at 1 damage after 2 rounds, and increase by 1 every 2 rounds up to 5 max.
---------------------
How do those sound?