You can add a logo image to the PDF from the iPad Photo Album.
To transfer the logo image to your iPad use iCloud Photos, Dropbox, email or iTunes.
Transparency is supported and recommended by using images in PNG format.
Tap Customize PDF
Tap Logo & Header
Tap the Change Logo button
Choose Select image from Photo Album
Choose your logo image
Adjust the logo size & text position as needed
Tap Done to save.
Make sure the option Settings > Invoice Format is set to PDF.