Can a couple specify in a separation agreement something other than 50/50 and have no trouble doing a QDRO after the divorce is finalized? Also, if there is a separation agreement then is there no ED order upon divorce?

You can agree to something other than 50/50. If the account is of a type that requires a QDRO then you will still need a QDRO in addition to the separation agreement. The separation agreement will serve as the basis for entry of a QDRO in the agreed upon amount.