Ah, found it. The following command will move TuneNet's AppIcon to position 200,200:
rx "ADDRESS workbench 'ICON root NAMES ""TuneNet: File Drop"" X 200 Y 200'"
I will leave writing a small commodity which monitors Workbench's root window for AppIcons and moves them on creation, as an exercise for the reader
(HINT: Query "GETATTR window.icons.all NAME root STEM root" and compare properties name, top, left and type (= APPICON))
I don't think there is any C interface for this stuff, but writing a program in C which fires off the appropriate ARexx commands isn't too difficult. It just needs a nice GUI which can list and snapshot icons.