The OP's issue was with blown highlights and too dark a subject (BIF).
It's tough to overcome in S or A modes with autoISO, so I was explaining what I do.
If I used M and set shutter and aperture but used autoISO - I'd also need to be able to set ExpComp to adjust for the camera metering the scene not the bird.
(Technically, this can be done by setting a button to switch the meaning of one of the dial turns to ExpComp, but, I don't like changing the meaning of dials on the fly)
As raythentic mentioned, spot metering should handle this if it meters on the area in focus, which there is an option for, and I've played with it a little.
By setting ISO, the ExpComp displayed while shooting M is just an FYI.
I'm no expert though. Perhaps someone can get nzmacro to throw in his two cents.