The first option is more complicated and likely more prone to errors as people may not realise that uploading a certificate is not the same as signing a document. It would be up to how this is done to make this clear. However it is better for people that sign PDF documents often, as once the certificate is uploaded signing is a simple option.
The second is easier to understand, as users only have to select one option to sign a document, but it takes more time (and may be annoying) if they have to sign many documents.
I would favour the first option, but you would still have to test the way in which you lead someone through the upload certificate and sign document process. That is going to be the most critical in this case.