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Once you've downloaded your optimised app, just unpack it and copy the folder contents to BOINC/projects/setiathome.berkeley.edu (the actual 'working parts' are the app itself and the app_info.xml).
Please do remember to stop BOINC first though...
If you have a large work cache it might be a good idea to run that down before changing over. (The last time I switched a rig from stock to opti-app, the switch over caused the work cache to be dumped.) | 
