You're fine booking two Flying Blue award tickets out of one account for you and a spouse. In fact, it's better to do it that way because it keeps you on the same PNR (passenger name record- which is like a virtual folder containing all the tickets for a party traveling together) and people flying on the same PNR are rebooked together as much as possible if your original flight is cancelled or you have a connecting ticket and a flight delay means you would miss a connecting flight.

You booking tickets for you and your spouse out of your own is pretty much ordinary and normal practice for any FF program you're likely to use.