How can I sign a document with a digital signature after securing the file?

If you need to sign document with a digital signature, you can choose to allow 'Filling in forms and signing existing signature fields' when secure a document and make sure that the signature field is already existing on where you would like to add a signature before securing the file.

 
You can add a signature field to the file in Foxit PDF Editor with the function shown below if there is no signature field. Then you can protect the file and click on the signature field to sign with a certificate.