It's important to use folders in a way that the materials inside them sit flat in the archival boxes. Make note of the score lines along the bottom edge of the folders. Use these, or create your own when needed, to fold each folder to the correct width for the papers included in each.
As you work through the papers, remove all paper clips, rusty staples, or anything else that is causing harm to the papers (you can leave any staples that are in good shape). If needed, a piece of acid-free paper can be folded in half and used to hold the papers together in place of the paper clip or staple. Do not use plasti-clips as they create many of the same problems as regular paper clips (creasing pages, creating bulk in the folders) and often break apart quite easily.