How does the checks and balances system keep the necessary and proper clause from being abused by a strong central government?

The system of checks and balances ensures that the federal government does not abuse the necessary and proper clause through the use of the judicial branch.

The judicial branch (aka Supreme Court) has the ability to rule federal laws/acts constitutional or unconstitutional. In other words, if Congress tries to overstep their boundaries in terms of what actions they can take, the Supreme Court can rule their actions unconstitutional. This ruling would prevent Congress from acting, as all US citizens regardless of political power must follow the ruling of the Supreme Court.