Hi Jeff,
The netkar 'root' folder is the folder where you installed NetKar. By default I think it's 'C:\NKPro11' (although you can change it at time of installation). For example I changed mine to C:\NKPro12.
'Root' refers to the base level of the specified folder (so inside that folder but no further down into any sub-folders.
So if for example you have a folder structure like:
C:\Program Files\Kunos\NKPro11\Tracks\Aviano\texture\
The root of 'c:\' would mean put file straight into Local Disk 'C:\'
The root of 'NKPro11' would mean put file straight into 'C:\Program Files\Kunos\NKPro11\'
The root of 'Tracks' would be 'C:\Program Files\Kunos\NKPro11\Tracks\'
etc
Hope that helps