Lightroom :: 4 Would Not Take Over Folder System

I have downloaded the LR4 trial. import from there into LR4 using the 'add' methos, then convert to DNG afterwards. I wanted to keep the same file structure, and have the photo's just 'referenced' by LR4
 
In Martin Evening's book it states: 'The add option is the one I suggest you use mostly here. With an "add" option you are telling Lightroom to "reference" the files where they are located on the computer.'
 
When I saw the 'reference' word I thought that LR4 would not 'take over' my folder system. But after importing one folder, I realise that although I can view the folders I haven't yet imported into LR4 with the Nikon View NX software I have been using with Capture NX2, View NX will now not read the one folder that I have imported into LR4.
 
This suggests to me that LR4 has indeed taken over my file structure - (I would like to keep my existing structure and open files from it in LR4 AND any other program I wish). Also, after I have imported all folders from my hard drive, it might be worth then importing direct from card.