I searched every where (almost) on the Net for an answer to this. Adding a secondary site collection administrator is very easy:
stsadm -o siteowner -url http://xxxx/sites/sitename -ownerlogin someuser -secondarylogin someuser2
Walla second site collection administrator added. If you have more than two site collection administrators you can add another by using this command:
stsadm -o adduser -url http://xxxx/sites/sitename -userlogin someuser3 -useremail email@example.com -role "Full Control" -username "someuser3Name Surname" -siteadmin
Now what do you do when you want to remove Someuser3 from the Site Collection Administrators?
1. Make a note of the user for the SecondaryLogin of the site collection
2. Add the someuser3 to the secondarylogin for the site. This will remove the previous secondarylogin for the site, and add someuser3 as the secondarylogin.
3. Add the user from step 2 (previous secondarylogin) back to the site.
This will remove someruser3 from the site collection administrators for the site collection.