PUM upgrade, Initial Pass or Move to Production?

We are wondering what everyone is typically doing when you apply a PUM using Change Assistant - Do you do an initial pass, finalize the package after customizations are reapplied, and use that as a MTP (Move to Production) pass for subsequent passes?  Or do you simply perform an initial pass for each subsequent environment and reapply your customizations with a saved project? 

We are doing a PUM upgrade but have a lot of moving targets with the length of time we'll be testing before go-live. 4 months spanning regulatory tax updates being applied to production, as well as other projects that we'll have track of in Application Designer projects, but want to make sure that even if we rolled them into the package to Apply via Change Assistant, that we will not overlay any configurations if we bundle the projects in the CA package doing and MTP, vs. selecting Initial Pass applying the additional projects separately after the Chane Assistant package is