If you are moving all of your DS3 Content to another dirive, there is no real reason to merge it with the DS4 ‘My Library’ folder, you can still keep it seperate if you want to. Just move it to a new location on amy drive, and tell DS4 where to find it in Preferences (Content Manager), DS can read DS content or Runtime libraries on external HDDs with no problems.
The one thing to look out for, is the ‘data’ folder in your DS3 setup. This folder holds all of the geometry files, and other files, that a DS3 Scene file needs to open correctly. If the data folder is not carried over along with the ‘Content’ folder, then you will get errors when trying to open previously saved Scene files. Just check to see if there is a folder called ‘data’ in the folder you are moving, and also check in the folder just above Content as well.
That is the only problem I can think of at the moment. Lots of people are trying out the new DAZ Install Manager, which will make downloading and installing content a lot simpler, but organising content takes time and patience. If you need more info, just post again.