Well, that and, by passing additional legislation.

There's two parts to this. The first is that in most cases, the issues stem from lack of clarity in existing legislation, or contradictions thereof. At anytime, if Congress does not like the way the Supreme Court ruled, they can pass different legislation.

The second stems in part from the first. If what Congress passed is interpreted as being unconstitutional by the Supreme Court, the States can amend the constitution.

There is no case where the Supreme Court can (in principle) simply make their own rules*

The debate and controversy comes where the Supreme Court is seen as making their own rules (or arguably asked to) because the legislative process is deemed too cumbersome or disadvantageous to a party. In my opinion, this is where a lot of the difficulties lie, in that the Supreme Court is asked to rule on matters that really should be more clearly legislated. But the issues are seen as easier/quicker to address by convincing 9 justices rather than two legislative bodies and a chief executive. Naturally, this brings it's own consequences.