In Account > Bank > Reconcile and click on the Name of your Bank Account (Blue Table) and change the postings explorer view to closed (X). Hold down the control key and click on Reconcile (this will highlight the colum) and type in your reconcile text. In your example, 20050701 will ahead of 2005062000 if the chevron (V) next to reconcile is downward and behind if the chevron is pointing upward.

In regards to your reconcilie coding in NV2, you could adopt something like 200506-01-01 for subtotal one and then 200506-02-01 for subtotal two etc. Just a thought.