Manual shooting is good, but I have never been in the camp of those who insist on it. I do a mix of Av and Manual shooting, more of the former but not that much more, call it 60/40. Call me lazy. But full manual is hardly necessary.
My first question is, whether the shots are correctly exposed and you are unhappy with what combination of settings the camera is choosing to get there, or are the shots incorrectly exposed. 1/1000 and f/5 and ISO 320 may be the right combination. Your language is a bit confusing.
I never shoot on any sort of variable ISO, I don't even know if that is possible (I have a Canon 50D). So I commit to an ISO first.
Actually, I'm not sure there is a second question until the first is answered.
