64bit ddr2 conflit with lan91c11

If the master and memory are on different clock domains then SOPC Builder will insert a clock crossing adapter. This adapter doesn't support pipelined transactions so your memory performance will drop a lot. To avoid this you can use the clock crossing bridge which will have a little bit more latency but it'll allow back to back transactions through it.

If you care about the performance of the Nios II processor I would suggest trying to operate the processor and memory at the same clock speed to avoid any clock crossing. Clock crossing transfers adds a lot of latency so keeping both cores on the same clock domain may give you better performance.