Effectively, no judgement is ever really final. This is because, in a democracy, we must constantly acknowledge that our judgement could be wrong. Separation of powers, as you correctly describe it, manifests that acknowledgement by providing an avenue to contradict every action. Congress can pass a stupid law, but the President can refuse to sign it and the SCOTUS can deem it unconstitutional. The President can sign a stupid order, but Congress can impeach him. SCOTUS can make a stupid decision, but the President can refuse to acknowledge it and Congress can rewrite the rules.
It's not easy in any case, and there are a lot of hoops to jump through. Generally speaking, each branch declines to take their nuclear option by acknowledging the implicit threat available and compromising beforehand. Obamacare and DOMA are both recent and useful case studies for this interplay; ignore the content and the rhetoric and just look at the mechanics of what each entity did and when and why.
It's not easy in any case, and there are a lot of hoops to jump through. Generally speaking, each branch declines to take their nuclear option by acknowledging the implicit threat available and compromising beforehand. Obamacare and DOMA are both recent and useful case studies for this interplay; ignore the content and the rhetoric and just look at the mechanics of what each entity did and when and why.