Hello Ken,
I am not a Nikon shooter so unable to give specific advice on Nikon hardware but I can make a few general observations. In rain forest situations you will usually encounter birds fairly close so the Better Beamer may not be necessary, depending upon the flash output power and the longest focal length of your flash zoom range. For example, I use a Canon 600EX-RT that is powerful and has a maximum zoom focal length of 200 mm. This works well in the rain forest with telephoto lenses from 300-600 mm focal length without the need for a Better Beamer. I previously used a lower-powered Canon 430EX II which has a maximum zoom range of 105 mm and with this flash I found the Better Beamer was useful. One of the downsides of the Better Beamer is that it can get snagged by vines, wire grass and other kinds of vegetation.
For opportunistic shooting in a rain forest situation I usually use what Nikon call ITTL flash. I use the flash to add about 2-3 stops of exposure to the ambient light exposure. That is to say, if the flash did not fire, the image would be 2-3 stops underexposed. The idea is to use the flash to make up the light to achieve proper exposure of the mid-tones. The camera exposure settings are adjusted manually, that is aperture (f/No) to suit the depth of field required, exposure time (usually the fasted shutter sync speed available, 1/200-1/320 sec), and manual ISO setting to achieve proper mid-tone exposure (usually ISO 200-800 depending upon the range to the bird and the available natural light). If you get the ISO roughly right, the ITTL will calculate the right exposure. For metering I use what Canon call partial metering which analyses the brightness of a field of view roughly equivalent to the metering circle one can see in the viewfinder. You may find that birds with particularly bright flashes of colour like the bright pale-green shoulder flash on the Noisy Pitta will over-expose so you need to pull back the flash output power a bit. This is achieved using some negative flash exposure compensation, say -2/3 stop. Do not use any of the camera exposure settings as all that will happen is the flash output power will be automatically increased by the ITTL and the result will be the same overall exposure. You must use the flash exposure compensation to get control of the overall exposure (not the camera exposure settings).
I hope one of our Nikon shooters can pick up the discussion and add more specific information.
Cheers, Ian.