Congress can regulate the number of seats on the Court and they can establish the types of cases the Court has jurisdiction over (other than those listed in the Constitution). Congress cannot establish the rules by which the Court operates any more than the President can regulate how Congress operates.
An important, underused check and balance. Eg. IIRC illegal aliens are eligible for loads of federal benefits not because Congress authorized that, but because some judge overturned Congress's banning of their eligibility. The solution requires two steps. First win WH and a large enough pro-American majority in House and Senate to pass the following. Then simply pass a new ban rendering illegals ineligible for the federal bennies and include a clause stating that wasn't judicially reviewable.