Gloshei,

With the freePatternWizard you can choose from a number of different stitches. Many of the larger pieces seem to be done in peyote, though loom/square stitch is also used. (Loom and square stitch basically look the same, but are completely different techniques.)

I haven't heard of anyone using the freePatternWizard for bead embroidery. While it probably could be used for that, my guess is there are other ways of using bead embroidery for creating larger pieces. It's a completely different technique, as it allows one to work outside of a grid entirely, so a grid isn't really necessary if you know where the different beaded areas should be on a particular piece. (I'm not terribly proficient at bead embroidery, so I can only say what I've seen and read about it, that bead artists who use this technique will generally plot out where beads should be embroidered on the fabric. There are likely some very talented people who can wing it and just figure it out as they go, but not being one of them, I'm not sure how well that would work for most!)