You can do either - just use the volume that's there when you take the gravity reading. As a simple example, say you have:
10 lbs 37ppg grain
1 lb 34ppg grain
You can use the equation:
gravity = efficiency * (10*37 + 1*34)/volume
Where gravity here is the last two digits of the gravity reading (i.e. 1.0xx).
So say you get 75% efficiency, then if you measure the gravity pre-boil (with a volume of 5.75gal) you should get a gravity of 0.75*(404)/5.75 = 53
If you measure gravity post-boil (with a volume of 5gal) you should get 61 (1.061 on the hydrometer).