I used to have them facing down, and had additional inline filters. One day the bike wouldn't start, until I thought it could be the fuel not reaching to the bowls. Blowing inside the tank put enough pressure to overcome the curves of the fuel line.
Now I have then facing up, as the fuel line runs directly across those two holes in the linkage plate, so the fuel runs straight into the bowl. I know that Archimedes would say it doesn't matter as long as the tank is higher, but I've found trouble and therefore I put them up. If you don't have inline filters I would say there should be no difference.