Instead of using the background file as a "seal", I would print the background file directly to the certificate. I use the following line to dump my company logo onto the certificate:
$pdf->Image("$CFG->dirroot/mod/certificate/pix/companylogo.png", 590, 425, 120, 50);
You should use a similar line for your complete background image (and move your image out of the seals-subfolder one level up).
Usually, all signatures and all seals have the same size (signatures and seals might differ). If you have one "seal" that covers the whole paper, then it will not work properly on other certificate types that expect just a small seal. As a seal, a teacher might select an other seal as a background.
On my certificates, I do not need any seals, so I copied all the signatures into the seal folder, deleted the old seals and use the seal as a second signature. Now I can choose different combinations of left signature and right signature.