That is correct!
You take the highest die on your side (which represents the thing your officer does that has the biggest impact) and you subtract the highest die on the other side (which represents the thing that has the biggest effect in opposition to you), and that's how much the task's strength is reduced.
(This of course assumes your officer rolled highest. If the threats rolled highest, you subtract the highest officer die from the highest threat die, and that officer loses the difference in Resolve.)
You will probably want to imagine the story results from this. Imagine the highest die overall being the determining factor in the fiction, and the highest die on the opposite side being the thing that was strongest in opposition to that.
Then, you can imagine the outcome. If you overcome the entire task in one roll, you might imagine your officer being a badass and just getting it done with impressive skill. If you have to make multiple rolls, you can imagine your officer struggling to overcome the mounting problems arising (especially if the threat dice come out on top a few times).
Also note that you don't have to perform the same roll if you don't reduce it to zero in one roll. For instance, you can have another bridge officer try something else, or use a different ship's system to respond. Or you can have a crew member assist on your next roll, lending one of their traits. (Later in the story, you'll get access to other bridge officers who will be taking on tasks themselves, and you'll be given the rules for officers assisting each other.)
Glad you're enjoying the game!