On horizontal pipe, "two-holing" a flange means that the bolt holes are oriented such that there won't be one hole at the 12 o'clock position, but rather a pair of holes, that are oriented such that the top two bolt holes are in the same plane. This is easily done with a level. If you look at something like a flanged gate valve (any manufacturer), you'll see that the bolt holes are oriented to match this configuration. If you didn't have this convention, it would be more difficult to align things. You'd look down a piping run, and valve spindles would be pointing off in all kinds of goofy points of the clock. It also lets valve manufacturers make the valve bodies with a shorter face to face dimension than would otherwise be possible. If flanges were one-holed, they'd have to leave space between the flange and the bonnet to get fingers and wrenches in there to do up the bolts. This can be tight enough, even with two-holing.