For screen printed items, the setup covers preparing a screen with the inverse of your design on it, carefully cutting out the design, and readying the ink.
For laser engraved items, it means calibrating your design into the laser.
A digital printing setup charges comprises uploading your image into the printer.
Heat transfer setups include printing your logo onto transfer material, and then transferring it onto your items. (Think a higher quality iron-on t-shirt transfer!)