There are SCORM content packages and SCORM Sharable Content Objects (SCOs). Content packages you can import directly into ATutor content through Manage>Content Import.
SCOs on the otherhand are standalone units that run in the SCORM player. You'll need to install the SCORM module for ATutor to use SCOs (admin>modules>install modules). SCOs do not become part of the ATutor content (though it might look like it).
As far as certificates are concerned, I don't imagine you will be able to issue a certificate after a test in a SCO, unless the SCO itself will do that. You can however, with the ATutor certificate module installed, issue a certificate after completing an ATutor created test. See the readme with the certificate module
http://atutorsvn.atrc.utoronto.ca/repos/atutor/trunk/mods/certificate/README