What I think you are asking is how to calculate a flow budget for constant head and well boundaries inside a particular area.
Firstly, the terminology in 6.1 for this type of flow budget is now called "rate budget". By default, the rate budget shows results for the entire model domain. To perform a budget analysis on a sub-set of your model domain (e.g. inside a shapefile or polygon), you need to create a nodal selection inside the area of interest and save the nodal selection as the target for rate budget analysis.
Instructions:
1. Select nodes of interest by drawing polygon or selecting by shapefile (see the help topic on selections if this is new to you)
2. In spatial units: right click Current node selection (under Node Selections) and choose "Store Current Selection"
3. You can assign a name to the selection and it is saved for later reference
4. Select the current node selection by clicking on it in Spatial Units
5. In the Rate Budget window, click the + symbol to add your node selection to the rate budget analysis
6. Click the "Active" tickbox
When your model runs, budget values will be shown for the current time step in the Rate Budget window
If you are running a transient model and you wish to store a time series of the budget:
7. Right click your saved node selection in Spatial Units
8. Under "Budget history charting mode", select "BCs"
During your transient model run, a chart will be plotted of the BC flow values for each BC type (1st and 4th). You can right click on the graph and save/export the data for further analysis.
Hope this helps!