By "Calibre folder" you mean the "Books" folder, right?
Don't worry, all the books will appear there. But SugarSync has been known to take much longer than Dropbox for the initial synchronization. Afterwards, the synchronization is a lot more prompt. For me, the first-time sync took a few hours, before the books were mirrored online. What does your SugarSync icon in the Mac OS/Windows status bar look like? If it's a green circle, then the books are still only being uploaded. If it looks like a little green bird -- only then are all of your files in sync and ready to be accessed online.
SugarSync isn't integrated directly within Marvin. So what you do is, you open the SugarSync app on your iPad, open Calibre's "Books" folder, and inside there, every writer will have his/her own folder, and then each work inside the writer's folder will also have its own folder. To me, that's very easy to browse, so I can quickly locate any book I need to load into Marvin.
I can also recommend you the excellent, free Documents by Readdle app. It allows you to access both Dropbox and SugarSync (and other cloud services) from the same place (one app). So, if you for some reason don't like the SugarSync app, you can also just open Documents by Readdle and access your SugarSync files from there, loading them into Marvin that way.
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