Since you moved the images from the external drive to an internal one, you need to tell LR where you moved them to.
The first thing to 'fix' is the moved/missing folders. Go to the Folders panel in the Library. If the Folders list is not a full tree like your OS tools show you, right-click on each folder and do a "show parent" until the full folder tree is shown.
From the tree select a top-level folder that has a "?", right-click and select "find missing" or "locate" (I don't recall the correct text). Navigate to the new location of that top-most folder. Repeat as needed for all your top-level folders. By fixing the top-levels, all the lower levels and photos will be automatically fixed.
I'm not sure exactly what you mean by "very difficult to navigate", as I haven't heard that complaint before. Could you be much more specific, and maybe even show us a screen capture?
There are detailed instructions for reconnecting missing photos in Lightroom. See: http://www.computer-darkroom.com/lr2_find_folder/find-folder.htm