Can I create subfolders in the Document Sync folder?

Yes. Pilots can add nested folders within synced Cloud Document drives for even more flexibility. Pilots can download individual documents, selected folders, or the entire Cloud drive, and receive automatic updates to the downloaded items, making it perfect for multi-pilot accounts where not all users need to download the same set of documents.
 
The folder structure is created with your cloud document service and will be automatically synced to ForeFlight Mobile. To learn more, visit: www.foreflight.com/documents.
 
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Folders setup from www.dropbox.com 
 
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Synced Cloud Document folders on iPad