If your existing blogs are wordpress 2.3 and higher than you should be able to add them as projects either one by one in Single Install or in a csv file and add in Multiple Install Blogs section.
You add them as if you were installing a new blog but instead of clicking Install blog, you [...]

UPGRADE INSTRUCTIONS:
In the CHANGES.txt file that is included in the WP ManagerDX package, find the version that goes after the one you already have installed. There is a list of files that were modified. Upload via FTP all the files modified to your /wpmanager on your host.
If the setup.php file is listed, then run [...]