Stacking them, which is co-locating them, gives you a 6dB increase in output compared to a single sub (assuming they are identical) But the bass response at your seat will be the same as having a single sub.
Seperating the subs will result in only a 3dB increase over just 1 sub. However the bass response will be smoother or flatter at your seat & across multiple seats.
Its a give & take issue. So it depends on what is more important to you. Have you measured your rooms response? If the response is decent & if you tend to watch/listen either alone or with one other person then you may want to keep them stacked. If you arent getting a good flat response at your seat or if you tend to have multiple people watching/listening with you then you may want to seperate them.
IMPORTANT!!
You cant just place the 2 subs in just any place in the room & expect an improvement in response. In fact, if they are placed wrong, you could get worse bass due to frequency cancellation. So you need to do a bass crawl, locate TWO good locations & place them in those two spots. Then you need to decide if you are going to have them Gain Matched or Level Matched. Also, try the 4 different Phase combinations to see which sounds best & blends best with your mains. Dual sub configuration can take some time to dial in & takes trial & error.