For those of you who do not know how to import your GEDCOM file into your existing tree: you can do this by uploading your GEDCOM file to http://www.geni.com/gedcom/start/ using a different email address than is associated with your existing tree on Geni. After the import is complete make sure your name (http://www.geni.com/profile/edit_basics/) is set the same on both accounts and then you can enter your other email address into your existing profile (additional email at http://www.geni.com/profile/edit_basics/) and it will ask you if you want to do a self merge, which will merge both accounts and trees. If it does not ask you to do a self merge, login to your other account and it will ask you if you want to merge trees.
Note: At this time any one GEDCOM file cannot contain more than 15,000 people. However you could break up the GEDCOM file and repeat this process using a different email address (or after the merge removing ONE email address from your profile to use). See http://wiki.geni.com/index.php/GEDCOM for known issues regarding addresses/locations, maiden names, and more.
Additionally note that you will have to spend lots of time running the merge wizards if there are lots of duplicates. See http://forum.geni.com/topic.php?id=23011 for my concerns and suggestions regarding GEDCOM merging, tree merging, and more.