There are two ways you can delete waypoints, routes and tracks from Atlas:
Drag your finger to the left across the arrow on the r.h.s. of the list item and a Delete button will appear. Press this to delete.

Switch off all the items in the list you want to delete (turn the button to red) – this can be done quickly if you want to to remove the majority of items rather than just a few by using the Hide All/Show all button.

Then touch the Delete Hidden button on the top bar of the list window.
The Waypoints, Routes and Tracks will no longer show on your maps.
When you connect your device to your computer via the inbuilt Atlas server you will find that any previously imported gpx or kml files will show up in the Points and Routes folders. However, if you have since deleted them from the waypoints or routes list in Atlas they will not be active. You can choose to leave them there or delete them completely.
If you want to re-instate a previously imported gpx or kml file then you will need to copy it into the folder again from your computer.
Always remember to keep a back up copy of the the gpx / kml files on your computer.
The tracks folder should only contain tracks which you have recorded using Atlas. If you want to import a track which you previously saved from either Atlas or another GPS device then this should be imported as a route.
We suggest you regularly copy your tracks from Atlas to your computer for safekeeping. Once you have done this delete them from the Atlas Waypoints, Routes and Tracks list and subsequently the Tracks folder you see when the Atlas server is connected to the computer. This will ensure a tidy system.