I haven't tried to embroidery on a shirt for a while, but I messed mine up when I did. I was having issues with the machine, and it may or may not have been the machine. It could've been that I didn't use a water soluble stabilzer on top of the shirt. I haven't gotten to try it again to see, but that may help you...?
When you put the onesie/shirt in the hoop like others have stated above and pull the back up out of the way, you may want to pin it there out of the way of the needle to be sure.