You shouldn't have to map everything yourself.
Since you are using the Harmony 1000 I would suggest you add the Game Console, Game Console with DVD, Sony PlayStation 3 device.
Go into that device and change the delays to all be 0.
Go into troubleshooting for that device and tell it the device sometimes responds to commands too many times or not enough.
Set the number of repeats to 0.
Change the button mappings for the device to set them up how you want them. The most important things to make sure to map here is the X command to the OK button, and the number commands to their corresponding number buttons.
Create a Watch a DVD activity and tell it you use the PlayStation 3 to watch a DVD.
Set up the activity for your devices (TV input, AV Receiver Input, etc.)
Change the button mappings for the activity. Make sure to map the X command to the OK button. Since you used the Sony PlayStation 3 device the color game icons should show up on your screen.
Go to the change options screen for this activity and disable the send play at start of activity, and send stop when leaving activity options.
Hook your remote up to your computer and update your remote.
These are the basic steps. I can't really get in depth because I am at work and I don't have the Harmony software installed here. If you need more help let me know and I can try to help tonight after work.