Logo is used by default with old template editor. If you use new one, please go to Design -> Documents -> Gift certificates: default page and add logo to the required place
I am having a similar issue to this, but it is in a multi store installation, When I am using the new document editor it is not possible to go to design/documents/gift certificates and add the logo as the changes effect all storefronts.
There is no way to save individual changes to each storefront.
I am unable to find a variable which pulls the store logos into the gift certificates.