Bless you, Jo, for your work for The Lydia Project. I am also a volunteer for them since 2009. I sew the Lydia totes, as well as retail bible covers, purses, and totes. I have embroidered a few toppers when they were cut too small, but mainly sew for them. Maybe I have even made some totes with the tops you made :)
Seems like you could align the embroidery for each topper in software before you send it to the sewing machine. I also have a 350 E and just got the 15000, so really am not any help regarding your question.
I just wanted to thank you for supporting The Lydia Project.
Judy in Eastern WA state