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Muizen, it is down to preferences, you have to work through what suits you. FWIW, I really dislike auto ISO, it is one setting I want control of all the time, so its on the C button for me. I set the main control - Aperture - first in composition so I shoot A mode, then seek the best compromise between the camera selected shutter speed and ISO, while checking the histo and working EC to finetune.
I got slack on the a99 initially and shot it at higher ISOs than strictly necessary quite often - revelling in the excellent IQ post a900 I guess - but now I know the sensor is so fabulous at low ISO, that is my aim in conjunction with an 'acceptable' s/s and chosen aperture.
The camera default choice of 1/80 sec cops some flack, dunno why, that is 2.5 times its true FL, you should be able to get good results there with good technique...'slow is smooth, smooth is fast' - so the snipers say.