The below I follow to make deployment life easy. Any suggestions appreciate.
1) I'll use Source and Target Connection as Parameter and set the value at Mapping Configuration.
2) I maintain same Connection names for Source and Target in all environments but the underline definition will vary based on the environment.
Connection Name 'Salesforce'
User: Dev Salesforce user for Dev instance, Test user for Test instance etc
3) Import only the Top level object like TaskFlow, that would bring all child level objects.
4) For any new changes I'll delete all objects and import as fresh.
5) Copy required physical files like parameter/batch what ever you need.