Chinook

I haven't built that specific kit, but have built lots of helo models.  I completely build the fuselage and glue in any windows that can not be reached from the inside after the fuselage is closed up.  I then tape up the window from the outside with either masking tape or blue painter's tape.  Place a large piece of tape over the window and press it tightly against the glass being sure to press around the frame outline so it can be seen.  Then simply cut around th frame with a sharp xacto knife.  If the window can still be reached after closing the fuselage (like on cargo doors, pilots' doors, etc.), I will leave the glass out and tape it up from the inside before tacking the door in place. 

Here is an example.

Front canopy, small jump doors, triangle window on pilots' doors, and chin bubble windows taped off from outside.  Cargo door windows, top greenhouse windows, and open pilots' doors windows all taped from the inside.

Hope that helps.

Another trick- I've done this on 1/72 aircraft including a CH-46:

put a blob of Elmer's on the window and work it around with a toothpick. It will pop off easily when you are finished.