Following tradition, in Christian ceremonies, the bride stands on the left side of the altar while in Jewish ceremonies, she is traditionally on the right side.
However, these days people are choosing to forgo assigned sides completely in order to bring together the two families and to allow people to sit where they'd like. You can still arrange the room with two sides and put out a fun sign with verbiage such as "Pick a seat, not a side. We're all family here once the knot is tied!" Pinterest has a plethora of fun sign ideas you can peruse.
However you choose to do it, make sure to let your ushers know so they can point your guests in the right direction.