The Desk Officer appeared from behind a filing cabinet with a pile of papers. The Desk Officer appeared, with a pile of papers, from behind a filing cabinet. Many of my sentences, I feel, can be written two ways. Is it just a matter of preference?
Yea. You can play around with sentences with loads of ways. And its not just a matter of preference but what you what to archive with the sentence. If you look at both the sentences in you example if fine. But the rhythm reading them will be different and have different effect. If we change it into something slightly more dramatic it will be easier to see that the sentence structure affects the mood etc. "The officer leapt out from behind the filing cabinet swinging a bloody axe." "The officer leapt out swinging a bloody axe, from behind the filing cabinet "
The first sentence is fine. The only reason why you would put a comma in there is if there was a natural pause and I can't see there being a need for one in the first sentence.
I think you're missing the point, which is that there are many ways to lay out a sentence. Which one the author chooses in a particular instance is a matter of choice, based on flow and rhythm, or emphasis, or clarity, or pure aesthetics.
It's also a matter of emphasis. In the second sentence, the reader focuses on the 'pile of papers' a bit more, e.g. perhaps someone had asked him to find out something, and the answer might lie in the papers he is carrying; or you want to show that the Officer is snowed under with work, that kind of thing. There is not an infinite variety of ways you could say this, but there are more than two, e.g. From behind a filing cabinet, the Desk Officer appeared, carrying a pile of papers. Out from behind the filing cabinet appeared the Desk Officer, with a pile of papers. --these give a feeling of surprise, like he's just popped out from behind the filing cabinet. You probably want to vary the structure and rhythm of your sentences anyway, to avoid that awful clunky monotonous drone you sometimes get with poor writing, so it's good to play around. You can try reading your sentences out as well, to see which you prefer.