(1) “Management wants this deal to close before the end of the quarter so that we can book the revenue this fiscal year.”
(2a) “Before the end of the quarter is when management wants this deal to close so that we can book the revenue this fiscal year.”
(2b) “So that we can book the revenue this fiscal year, management wants this deal to close before the end of the quarter.”
The most emphatic position in a sentence is the end. The beginning is the second most emphatic. So if a close by quarter’s end is that point that deserves the most stress, don’t bury it in the middle of the sentence, the way (1) does. You can highlight the important point by placing it at the start of the sentence (2a) or at the close of the sentence (2b).