Confused about surround modes - does it automatically choose TrueHD or whatever is best? Or is Prologic II where I want to be?
if you don't change anything, as long as input/decode mode is still set to the default "auto" it will automatically detect the input signal. For any multichannel content it should play automatically (e.g. "Dolby Digital" for a DD 5.1 signal, "Dolby TrueHD" for a DTHD signal, etc). This is called "Standard" mode -- pressing the "Standard" button on your remote will always return it to this default decoding mode with multichannel material.
With 2 channel content, you have your choice of leaving it in stereo, or matrixing it to 5.1 (with PLII or DTS Neo, your choice). With a 2-channel input, the "Standard" button will cycle between PLII > NEO. The D/ST button next to it will cycle between DIRECT and STEREO modes.
For more info you should read the audio section of my faq: http://batpigworld.com/fadq.html#audio
If you change the surround mode with a given input signal, it will remember your preference (e.g. if you like a stereo PCM input to play in STEREO mode, it will remember that the next time it sees a PCM stereo input). Note however that if you use the QUICK SELECTS to change sources you will have to re-memorize it or it will go back to the defaults next time.
It memorizes these surround preferences separately per input; this is "auto surround" which is on by default. If you want to check what the current preferneces are for that input, open the OSD and check AUTO SURROUND in the INFORMATION menu.
Also, for music CDs and Ipod, is there a way to have just left, right and sub?
yes, both STEREO and DIRECT mode can be configured as 2.0 or 2.1. You will want to use the 2CH DIRECT/STEREO menu to set up your preferences; this is covered in the link to faq, above.
Possibly also have the surrounds be a clone of the left and right fronts?
there is a 5CH STEREO mode (this is one of the "denon simulation" modes accessed by the "simulation" button on the remote. However, it will mix content into the center channel.
another option is to use PLII but switch to the MUSIC mode (this must be done via the OSD after using the Standard button to turn on PLII). You can change the amount mixed to the center and the surrounds using the CENTER WIDTH and DIMENSION controls. If you turn the CENTER WIDTH all the way to the extreme, it will mute the center channels and give you 4.1.