Assuming no DOAs and the board recognizes everything just fine, the 2 x 8GBs would be preferable.
That is a big assumption, though, because a lot of boards just don't recognize 8 GB sticks at all and a lot of boards or sets of RAM have 1 stick or slot with a problem that causes huge problems to troubleshoot starting at day 1.
Is there any good reason you need 16GBs instead of 8 GBs?