Need some help to use altdq and altdqs megafunction.

Cyclone II did include a delay-circuit for DQS. Cyclone III and IV do not, so you have to ensure this delay by routing/constraints.

BTW: I think, the Altera-phy does rely on the DLL in the DDR(2)-memories (not in Mobile DDR!) which ensures that the DQS-phase is close to the memory-clock-phase. Additionally it fine-adjusts the capture-clock with the phase-shift-functionality of the FPGA-PLL by calibration. As far as I know, it does not use DQS for capturing the data.

Thomas