The setting for the backup doesn't matter per CS, unless something has changed. CS has pretty much stated the only fatigue setting that matters is what the starter is set at. The reason is, once the starter's fatigue level reaches it's setting he will be subbed back into the game. So for example you have your starter set to fairly fresh and your backup at getting tired, and your backup will still likely be taken out when he is fairly fresh because your starter should be back to fresh by then.