Windchill sees EVERYTHING. All relations in the Cad model will be captured and stored so things are kept in sync. You want to make sure you lock items when you add them to the workspace that you are specifically not wanting to checkout. This will stop Creo from checking them out when a regen modifies them but you will be asked...once.
Next step is to look at your designs for potential regen issues. Avoid using circular dependencies and watch out for relations that change upon regen often. For example, we had a family table that had a relation which would change a parameter when opening. We cleaned that up by adding the parameter to the family table which made it static and stopped the mass checkout.
