Does it work in a 5.1 configuration?
Do you have all 7 speakers connected simultaneously in addition to the subwoofer?
That's necessary. The system won't work properly if only some of them are connected.
Perhaps the quickest thing to do is to reset the receiver (see page 117 of the owner's manual) and start over.
After resetting, start on page 40 of the owner's manual and go through the "first time setup" procedure step-by-step in order, including the "auto setup" which runs Audyssey and detects the speakers. Trying to do things manually or out of order usually is an exercise in futility.
For example, if you started with a 5.1 configuration of front (left and right), center, and side-surround (left and right), you would add surround-back (left and right). If the side-surround speakers (called just "surround" on page 18 of the receiver's owner's manual) aren't connected, the surround-back speakers won't be detected.
Marantz SR7009/7.1.4/FH+TM/DefTech PM1000/LCR+TM amped