Yes, the book-a-window-and-aisle trick is usually a good way to maximize your chance of having an empty seat between the two of you. Be forewarned, however, that there is a slight chance you will come across someone who refuses to switch seats. I have seen posts by people on Flyertalk who hate the window-and-aisle-bookers so much (for "unfairly" taking away good seats and leaving only bad ones for single travelers) that they will refuse to move, just to spite the couple who wants to switch.

I doubt that on a long-haul flight anyone would be that spiteful and not take a window or aisle over a middle, but you never know.