Does your seconddomain.sh reference your seconddomain.conf? If it does you should be able to put the desired properties in seconddomain.conf.
You should only need to set jboss.domain.base.dir; the other properties you are setting are all set to the default values they would have if you just set the one property.
Perhaps your problem in a typo? It's "jboss.domain.base.dir" not "jboss-domain.base.dir". No '-', all '.'.
From what I see you only need to set "-Djboss.domain.base.dir=/apps/jboss/jboss-eap-6.4.0/seconddomain/" (correct the typo Brian already mentioned)
no other property needed, also specifying --domain-config or --host-config is not necessary as you set the default.
Other properties, for server-groups or server I would add as system-properties to the domain.xml or host.xml to have all in one place.