Two notable points:

MBTA made the "2 bus plus rapid transit" transfer within 2 hours available about a year ago. So, at most, you only pay the "subway" fare portion for a 3-vehicle ride.

As you swipe in/tap in, keep an eye on the LCD display on the farebox/turnstile it DOES display your remaining balance as you enter.

When in doubt, a Fare Vending Machine is your friend. Just press the "More Info" softkey to read your balance.