To upgrade the library in MCNP5, users should place the new ACE files in the MCNP_DATA directory and modify or replace the xsdir file that indexes them. It's advisable to stick with the same standard cross section library for a specific MCNP version to maintain result consistency and reliability. Using different libraries may lead to discrepancies in results or even program crashes. Trust in the software's results is emphasized as a key reason for using MCNP. Proper library management is crucial for accurate simulations.