I've done it two ways. You can put just a little air in the tube, then slip the stem through the hole as you tuck the tire into the rim recess, Then if you're lucky you can work the rest of the tire over the rim, both beads at the same time.
Most of the time I slip one bead over the rim, then insert the tube with the stem through the hole, then push the other bead over the rim. A little air in the tube helps to keep the tube from having folds.