Use a 1/2 cross-stitch and run floss through bead.  Be sure all stitches slant in the same direction.  This method will cause beads to lay diagonally.

Use a regular full cross-stitch.  Run floss through bead when working both "legs" of the X.  Depending on the direction of the X, the holes of the bead will lay side-to-side or top-to-bottom.

Use a "split" cross-stitch.  Run floss through bead when working first half of X.  Work second half of X by laying floss across top of bead and split floss on either side.  This causes the beads to lay diagonally, but holds them a little tighter than the half-cross method.