The HealthFrame v2 data model only supports tracking of medical expenses, and not tracking transfers into accounts (which is needed to compute some of the things you are talking about).
Future versions of HealthFrame will support a more elaborate data model, so you can track accumulation of funds in a health savings account, adjustments, etc. And we will provide better support to relate a single expense to a particular event (say a visit etc).
For now - all that you can very effectively do with HealthFrame v2 - is to track medical expenses.
As for the best way to link conditions, visits etc, just create relationships using the 'Related Information' panel. Future versions of Healthframe will take better advantage of this information, allowing for better reporting, filtering, and searching.