hi derek, this is one of the topics that we cover in our flow training and mentoring program.
overall, you just need to be diligent with your changes. if you change a dimension in a part, you need to make sure it is set to "this configuration". then at the sub assy level, you have a new config for that change. then at the top level assy you have a new config for that sub assy. if you do this, then your results will be conserved. in these cases you would not choose "current config" unless you were cloning from that new config. most users work flow is to clone to a new config and make the changes.
Thanks a lot, Jared. That made sense.