Beads during or after stitching doesn't matter. Most choose after as the beads are fragile.
Two ways to attach. Use a single strand the color of the fabric, or close to it. Many books say to use a 1/2 cross. This will make the beads slant, but that's OK. Either direction for the 1/2, but I've seen more that used 2nd leg, or course of a x-stitch.
The second way is to do a full cross, going through the bead twice. A little experimenting will show you which way to put the needle through the bead. I use this method because the beads stand upright.
Mirabilia normally gives the beads their own squares.
If beading as you go, be careful not to smash the beads -- a problem with hoops & scroll frames. I use a frame & pad the beaded fabric on the rod with batting or paper towel.