The setup fee is a one-time charge per logo. It covers the time needed to adapt your artwork for embroidery (digitizing / stitch preparation) so it can run correctly on the machine.
You only pay this fee the first time you order a given new logo. Repeat orders with the same prepared logo typically do not need the same setup again.
If you are uploading a new logo file but do not select the appropriate setup fee option when it applies, we may need extra production work and additional charges may apply. When in doubt, choose the option that matches your situation or contact us before ordering.