The manual is confusing because the machine is complicated and many features can be controlled in different ways. Forget what the manual says on page 43: the recorder defaults to stereo audio recording unless you change from "Stereo" to "Dual Mono" in the Home Menu>Initial Setup>Audio In setting.
If that setting shows a yellow mark next to the word "Stereo", the 660 is recording in stereo. If it shows a yellow mark next to "Dual Mono", switch it back to "Stereo".
You'll just have to trust me on this, I've been using these Pioneers for five years and there are times when you have to ignore the manual because it speaks nonsense. There are times when you have to ignore the onscreen display because it is misleading. This is one of those times. You do not
have to worry about the machine recording in "Dual Mono" in timer mode just because those words show in the Timer screen: as long as that screen shows five dashes ("-----") next to the words "Dual Mono", the unit is actually set to record in stereo
It seems a bit scary that the Timer screen shows the words "Dual Mono" all the time, because if you try to change the setting when it shows dashes (-----) you can't: the arrow keys jump right over "Dual Mono" to highlight "Video Mode". Again, this is because "Dual Mono" is not turned on or off in the timer screen: it is turned on or off using the initial setup menu. If "-----" is visible in the timer screen, "Dual Mono" is disabled by the Initial Setup controls and Stereo recording is the default. You cannot switch to "Dual Mono" audio in the timer screen, not even by accident: the machine prevents it.
Look at it this way: the "Dual Mono" field in the timer screen is a status display only: it isn't normally adjustable, but it reflects the setting you make in Home Menu>Initial Setup>Audio In. The Pioneer interface is generally very nice and understandable, but it does have a few areas where it works the way engineers would like instead of what we users would like. To you or me, the logical way to display Dual Mono status in the timer window would be to show "OFF" or "ON" next to it, or better yet change the words "Dual Mono" to "Stereo" when Dual Mono is off. Instead, Pioneer chose the geeky engineer's language: dashes ("-----") to indicate a feature is inactive. Because, you know, normal people like us would know exactly what that means.