After installing Dropbox on a new computer make sure that the Boxifier folder is checked in the Selective Sync settings in Dropbox and all the subfolders are unchecked. Then you can go and right-click a folder to relink it. Choose "Boxifier - Sync with Dropbox" and a window will open. If the name matches an existing folder in your Dropbox then you will see a green Relink button in that window.
Do this for all folders that you want to relink.
Then, after you've right-clicked and clicked Relink for all those folders you can go to the Selective Sync settings in Dropbox and check them so they start syncing with the folders outside of Dropbox. That's all you need to do.