A couple of basics ... just in case:

1. Unless something has changed you WILL need the dummy plug.

For MOO:
2. Moo uses ALL ATI GPUs so you will only show 1 task running in BOINC.
BOINC should show: running (??cpu + 2 ATI GPUs)
3. The time reported in the task listing on the Moo project may or may not be accurate when running multiple GPUs. Click on the left column of a pending or valid wu (opens the wu std err file) and look at the START time and the STOP time and the difference is the actual time it took to do the wu. Your reported time MIGHT be double what this says. The wu has the correct time.

What I mean by this: I recently put a new 6990 on a friends account and it was reporting 784s to complete a wu. After several days I detached/reattached and moved it onto my account. It started showing 1570s per wu while the std err file still showed it was completing wu in 784s. Same machine, same card, and same credits being produced ... it just showed double the amount of time in the projects tasks listing.

4. When you have it running Moo, check the GPU loading using something like GPU-Z and you should see 95%+ loading on both cards.