1) If you ignore any forces acting on the projectile (and for basic courses and simplicity you usually do) or consider them to be zero, then yes.
2) If your initial position is zero, then yes. In a question where a projectile is dropped from a height (one that would have a "release point") typically you would use that height as the initial position.
Edit- The "Y" would be instantaneous position in the y component. The initial "Y" would be inserted on the right side of the equation. (Y = Yinitial+ Voy*t - 0.5*9.81*t^2)
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