How to utilize programmable delay chain?

I believe D1 is what you want. The TimeQuest report annoyingly doesn't have a separate line item for this delay chain so you don't see it explicitly, but the delay values should change. If you locate the input pin from the fitter report or a timing report to the Resource Property Editor, it is explicitly done there.

That being said, the fitter should automatically set it for optimal timing. I normally just enter timing constraints and that's all. I just threw down a quick input -> output design in Cyclone IV and the Fitter Delay Chain summary clearly shows a Pad to Core 1 delay chain and it's set to 6. (Cyclone IV doesn't have explicit input DDR registers, it just quickly drives the LAB next to it, which is just about the same speed)