How to add substitute item in the Bill of material........How will it reflect in the work in process

We are creating the BOM containing lets say 5 purchased item.Out of that, one item is having substitute option.This item can be substituted with another item.

Now we want to know how to attach the substitute item in the  BOM.After attaching the substitute item in BOM, it will have implications in work in process.

We also want to know, while completing the descrete job, where will this substitution reflect? where can we change the main item with substitute item in work in process. 

Can you privide metalink ids which will tells about this topic.