You can make a single part out of 2 or more parts that have overlapping geometry and are of the same material. The merged part can be edited to add or remove parts.
 Part panel
 Part panel  
  (Merge Parts).
 (Merge Parts).  Part panel
 Part panel  
  (Edit Merged).
 (Edit Merged).  Merged Parts panel
 Merged Parts panel  
  (Add) or
 (Add) or  (Remove), and then select the parts to be added or removed.
 (Remove), and then select the parts to be added or removed.  (Finish Edit Mode).
 (Finish Edit Mode).  Part panel
 Part panel  
  (Edit Merged).
 (Edit Merged).  Merged Parts panel
 Merged Parts panel  
  (Add) or
 (Add) or  (Remove), and then select the parts to be added or removed.
 (Remove), and then select the parts to be added or removed.  (Finish Edit Mode).
 (Finish Edit Mode).