From now on, when you import from your hard disk, you should select ADD instead of COPY or MOVE. This will keep the photos in the same folder.
As far as the existing problem, if you have done any work on these photos in Lightroom, importing the photos again will create a brand new copy that does not have your edits or metadata applied to the photo, and will just cause confusion because now you have two copies of the photos. Better you should use Lightroom to move the photos to the desired folder, rather than having two copies and causing confusion. AN EVEN BETTER SOLUTION is to assign keywords and other metadata to the photos and forget about folders entirely, let the keywords and other metadata be your organization method and your search tool.
Advice: Never re-import, this causes more problems than it solves.
Thanks DJ Paige - I have found the images in the all photographs catalogue and have given them a colour label.
I want to import the to a collection now to start working on them again - can/How do I do that?
Sorry if Im sounding a bit dense/
You don't need a collection to start working on them. Although you could select the images with the color label (use the filter bar) and then create a new collection and tick the box that says include selected images.
You ought to start looking at beginner's material on Lightroom rather than trying to figure out all of this yourself.