Another option instead of crossing the shock cord bungees, is to put clips on longitudinal bungees to allow them to clip together in the middle.
I first saw this on the Mariner boats:

There are a couple of advantages with this arrangement:
1)The bungees are slack when not in use, which probably increases their life
2)You don't have to 'work' the deck-stored object under the bungees, but can put it down and clip the bungees over it.

Of course, you can leave the bungees clipped in an 'X' if you wish.

Also, I recommend making your deck attachment points as versatile as possible by providing for multiple line and bungee attachment. If you have already decided on Maroske-style holes in the deck, threading some thin, high strength Spectra cord loops through the holes will provide some more attachment options. IMO larger recesses with bars across,or even pad eyes are better than Maroske style....

Remembering that shorter bungees have less elongation, my preference would probably be for fewer and wider-spaced 'X' bungees, but it depends on what you are thinking of stowing on deck.