One very popular format is MP4 with the h.264 codec. This provides low file size with excellent quality video. Digital Media Converter Pro can convert the VOB files on your DVD. If you are converting multiple DVD's, I recommend using Rip DVD Plus. It is designed for converting DVD's. The default settings in Rip DVD Plus will give you excellent quality output. It is as simple as loading your DVD and clicking the 'Rip' button.

Please edit your automated transfer profile. Under 'Select Files and Folders to Exclude' click 'Configure'. Now, check the 3 subfolders you wish to exclude. This will only transfer the files in the root. You may also be interested in reading about filtering. This is useful when you only need to transfer certain types of files. More information on configuring filtering is available at this link: https://www.deskshare.com/help/AFM/Filters.aspx