First, check to see whether your machine lets you adjust the foot pressure. Some of the new machines have a few different settings to accomodate especially thick or especially thin fabrics.
If you have a walking foot (even-feed foot) try using that, too.
If you can't adjust the pressure, or if adjusting doesn't help, try putting paper underneath your layers as you feed them through.
If you're sewing fleece to fleece and using paper underneath doesn't work, try putting the paper on top (making sure to line up the edges of the paper and fabric so you can maintain the proper seam allowance). As a last resort, try sandwiching both layers between two pieces of paper. You might need to pin it all in place first. (Or iron strips of freezer paper along the edges. If you have to apply it to both layers, you'll probably still need to pin first.)
I guess you could also try using a darning foot - as though you were doing freemotion machine quilting. I could probably never pull that off because I couldn't keep the seam allowance even, but you might have a steadier eye and hand than I do.
If push comes to shove, stitch by hand. A lot slower, but it'll get the job done. ;-)