Always make sure that you have the latest version of Studio One 4 or Studio One 4 Artist, as ATOM was first supported in Studio One version 4.1 and up. If you are on the latest version of Studio One and the software fails to see the ATOM, you can go to Preferences>External Devices to see if your ATOM shows up. If it is there, make sure that "Receive From" and "Send To" are both set to "ATOM". If it is NOT in External Devices, then click on "Add", then select the PreSonus folder on the left-hand side, then select "ATOM" and set the "From" and "To" as mentioned before. The Studio One logo should change from Green to Blue when connected.
For ATOM to be able to control an instrument or effect, the track must be record enabled in order for MIDI to be sent to the plugin(s) (also make sure that the "MIDI in" is set to "All Inputs" for that track). For the knobs to control parameters, "ATOM" must be selected in the upper right hand corner of the plugin and YELLOW (active). If you use multiple MIDI controllers, it is possible that the other controller is assigned to the plugin currently (like a FaderPort for example). Click on the drop down arrow to the left of the controller name, and select "ATOM" if it is not currently selected and then click on the word ATOM to activate it once it is selected.
If the ATOM is not being seen at all by other software and Studio One, then you should try using a powered USB hub as not all computer USB ports are created equal. The unit may not be getting enough power to function properly.
NOTE: The pads and buttons will go dark when the Create a New Song dialogue box is displayed. This is normal, as you will be using your mouse to setup your songs initial parameters. Once a new song is created, the pads and buttons will turn on and function.