First, you have to inform Finder that you want iToolBox to open these files. To do that, open a Finder window, navigate to a folder containing .ato and/or .elx files, and on one of them. Select Open With / Other... You'll get this dialog:
When the file dialog opens, change the Enable: drop-down to read All Applications , then select iToolBox, and check ✓ Always Open With
At this point, iToolBox should start and open the file, and will continue to do so in the future.
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