links for multisites

it shows up on the subsite, and google is indexing on the mydomain link. example http://seoforbeginners.info/empirebuilder/triathlontrainingplans-org/sprint-distance-triathlon/ was indexed quickly, but http://www.triathlontrainingplans.org/sprint-distance-triathlon is not indexed and sort of defeats the point of having the url http://www.triathlontrainingplans.org Does that make sense? Sorry, but im not really explaining my self well.