I just got an iPad so I'm transitioning my comic reading from my Windows laptop to the iPad. On Windows, I use a fantastic comic reader called 'Cover.' All of my comics are on a shared hard drive connected to my router, that I have mapped to a drive letter in Windows Explorer. Cover sees the comics, scans for updates upon starting, and shows a lovely grid view that includes folders, showing the cover of the first comic in that folder.

I don't know how other people organize but I can't have all comics loose in one folder. Batman comics are in one folder, Walking Dead in another, etc.

YACReader shows all the folders in the left pane, but the right pane only shows the comics in the folder being views. There doesn't appear to be a setting that shows the subfolders in that folder - is that correct?

The left view can show folders and subfolders, there is no limit in the number of levels...plus it gets filtered when the search is used.

can I see an screenshot of how does YACReaderLibrary look with your setup?