Nick:
I think that the number provided by default for a new waypoint will be one number higher than any other numbered waypoint that is present on the GPSR at the time you create the new waypoint.
So - if you want to have the GPSR start numbering newly created waypoints from 001 again, go through your GPSR waypoint memory and change the numbered name of any existing waypoints that were given a number by default to something else - typically a text name - and then the GPSR will start assigning numbers from 001 again.
An easy way to do this is to upload all your waypoints from the GPSR to a MapSource file, save that file (with a name such as 'Upload June 1 before editing'), then do a 'save as' of that file with a different name (e.g. 'Upload June 1 after editing'). Once you do the 'save as', you will be working with a copy of the file, not the original. Make all the changes you want to the waypoint names within MapSource - this is easier and faster than trying to change names on the GPSR itself. When you are finished, erase all the waypoints from your GPSR, then download the 'edited' waypoint file to the GPSR. All will then be nice and fresh and organized on your GPSR.
The reason you have to first erase the GPSR's waypoint memory is this: If you have a waypoint there called '026', and you modify it in MapSource and call it 'Nick's Pub', if you then download it to the GPSR without erasing the GPSR waypoint memory, you will then have two waypoints in the same place: The original 026 and the new one with the text name.
Let us all know if this suggestion works for you or not.
Michael