I still cant get it to work the older faster way. After hours of looking this is the way i have chosen to do it.
"Setting up Calibre Server and OPDS in Marvin"
http://blog.marvinapp.com/post/49081628921
It lets you do it over your Wifi while calibre and marvin are running. You can download one at a time but its not really that long. That is unless your like me and have whole collections of stuff i want to read when the mood strikes so i'm constantly changing whats on my ipad. I really really hope someone can fix the old way.
Hope this helps some