I'm a beginner myself but I believe you need the timing info from the memory chip datasheet and use these in the sdc constraints so that the fitter can optimize the paths to accommodate the latencies.
The numbers in both DDR-400 and DDR2-400 stand for the maximum amount of transfers per second which is the same 400MT/s for both modules.
For DDR this gives a transfer rate of (internal memory clock rate) × 2 (DDR) × 64 (number of bits per transfer) / 8 (bits per byte)
For DDR2 this gives a transfer rate of 2 x (internal memory clock rate) × 2 (DDR) × 64 (number of bits per transfer) / 8 (bits per byte)
But since the internal memory clock of DDR2 is two times lower, they both result in the same throughput. For both modules, the externally applied I/O clock rate is 200Mhz for both modules.
In short, DDR-X and DDR2-X memories with the same value X have the same maximum data rate and the same externally applied clock rate of X/2. Difference is that the internal memory clock of DDR2 is two times lower than the one of DDR and most likely some differences in internal latencies.
N.