The best place for handset specific questions is the sub-forum for your device - Motorola Atrix 4G - Android Forums - other users have quite often experienced the issues you may suffer from and are therefore the best to help out!
It will take a few power cycles before the phone will accurately report a charge. If you want to optimize that process I'd recommend doing a deep power cycle ...
Discharge the battery until the phone shuts itself off.
Recharge the battery to full using the a/c adapter, not a usb cable.
When the phone shows full, unplug it and reboot.
Plug the phone back into the charge and shut the phone off while plugged in. Even if it shows full, let it charge for at least one more hour.
Unplug the phone and reboot one more time. You should see a significant increase in battery life.
What you are doing is not conditioning the battery, but teaching the phone the batteries' capacity. Be advised that you should only need to do this once and that regularly deep discharges can damage Li-Ion batteries.
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