I use a slightly different setup/gear a Nikon D50 w/80-400VR handheld.
1. When using a tripod leave the VR (Vibration Reduction) off.Image Stabilization & vibration reduction lenses look for vibrations in your camera in order to reduce it. If they don’t find any they actually can cause it, & as a result actually cause camera shake.
* I would shoot that lense handheld with VR/Stabilization on for flight shots if you can, much easier to follow a flying raptor and shoot than trying to move a tripod or monpod head to keep up.
2. When shooting flying birds let the camera do the work for setttings selection, you don't have time to keep playing with the settings.
*You paid good money for the gear it is quite capable of giving you good results, concentrate on the moving bird instead.
3. Not sure what the setting is called on your body but I use AF-C which focuses continuously while shutter button is pressed halfway.
*This is a must setting for getting good flight shots.
4. Changing setting other than manually adjusting the exposure depending on lighting is all you should need to do to achieve decent results.
* Go out and practice on some birds IE: Gulls etc before you go and check out your results at home. This will give you an idea of how your doing.
5. Focus point single is the best for flying birds. Try to aim and focus on the head instead of the body, will give you better results and less post editing. Of course this is not always possible so the body is fine, but in a controlled enviroment this should be fairly easier to do.
Here is a sample of a flight shoot taken recently with my camera in P Mode (camera picks all the settings); AF-C with VR enabled handheld. Lighting was okay but not ideal.
Sounds like your flight shots will be more at eye level which is fine, forget about the background and focus on the bird you'll rock it out. The 3 shots below are by no means excellent but with an older 6MP camera thats about all I can manage.
Scaup in flight
Red-tailed Hawk
Snowy Owl
To summarize:If using a tripod leave the VR off, for handheld leave the VR on.
Let the camera body select most of the settngs automatically (my personal preference alot of shooters like to adjust settings which is fine)
Select Auto Focus continous along with single focus point.
Focus on the raptors head. If you are not able to do this, go for the body. No point is loosing the shot of a small detail like this.
Don't worry too much about the background, sounds like a static location so the background is most likely preselected for you.
Sun position should be behind you or even slightly off the to the side.
Depending on lighting you could manual adjust the exposure + or - in small intervals as needed.
Practice before you go but most importantly have a great time doing it
