The study score reflects your overall position in the subject relative to your peers, and is out of 50. It's on a bell curve, so roughly 2% of the people taking that subject will get 45+, roughly 10% get 40+, roughly 25% get 35+ etc.
Your study score is calculated using your scores for GA1, GA2, & GA3. The VCAA website lists what these are and how much each contributes to the final score.
For example, in biology, GA1 represents Unit 3 SAC performance (worth 20%), GA2 represents Unit 4 SAC performance (worth 20%), & GA3 represents exam performance (worth 60%).
It's important to note that your SAC scores are moderated, and VCAA doesn't care about the percentage mark you get on SACs, rather, they use your rank and how well your cohort does on the exam.
3. Scaling is applied after everyone's study scores have been calculated. If most people who are studying subject A get a higher score on their other subjects, subject A will be scaled up to reflect its difficulty.
4. Generally ATAR calculators use your raw (unscaled) study score prediction.
They're pretty accurate if you're good at guessing what your study scores will be - but it's difficult to guess those, so I wouldn't spend too much time playing with the calc.
5. Look at the marking report for your subject in the previous year and see what grades your predicted marks correspond to.
(There are much better guides than that short description in the technical score discussion section of the forums - if you really want to learn the mechanics I'd recommend looking there)
6. Depends what subjects you're studying & the strength of your cohort