I just bought my first PMD661 (new) and, in my first tests out of the box, encountered hand noise on the recording, both from simply handling the case of the recorder and from touching the record level pot.
This happens both when using the internal microphone and with a Beyer omni connected via XLR.
With the internal mics, you'll have this. Do me a favor, plug in the beyer omni and a pair of headphones into the PMD661. When you record, tap the beyer to make certain that the handling noise you're hearing is actually coming from the beyer.
Please consult your new manual. Page 18 and 43 should describe in detail how to operate the PMG661 with an external mic.