...how do I save them after I tweak them in RAW? the originals are no longer there, in their place is the one I worked over
You can't 'save' a Raw.
No changes were made to the pixels in your original. Camera Raw is a parametric editor that adds an XMP data file to the Raw data file.
The XMP data file has the instruction that tell the edit rendering engine (Camera Raw) what slider and tool adjustments you made.
In the Camera Raw preferences you need to decide if you want that XMP file embedded in the Raw data or if you want to leave in the default setting that makes the XMP file a sidecar.
If you have the XMP file as a sidecar and then want to move the Raw file, you have to move the XMP sidecar file too to keep the edits you made with the image.
I highly recommend you get the inexpensive (used from $0.01 + $3.99 shipping) book: Real World Camera Raw with CS2
Amazon.com: Real World Camera Raw with Adobe Photoshop CS2 (9780321334091): Bruce Fraser: Books