If you put State and City not both in the rows, you’ll get separate margins. Reshape and you get the table you’re after:
In [10]: table = pivot_table(df, values=['SalesToday', 'SalesMTD','SalesYTD'],\
rows=['State'], cols=['City'], aggfunc=np.sum, margins=True)
In [11]: table.stack('City')
Out[11]:
SalesMTD SalesToday SalesYTD
State City
stA All 900 50 2100
ctA 400 20 1000
ctB 500 30 1100
stB All 700 50 2200
ctC 500 10 900
ctD 200 40 1300
stC All 300 30 800
ctF 300 30 800
All All 1900 130 5100
ctA 400 20 1000
ctB 500 30 1100
ctC 500 10 900
ctD 200 40 1300
ctF 300 30 800
I admit this isn’t totally obvious.