You get the Vy from this equation:
y = h + Vy * t - g * t² / 2
If you know "t" (time of flight), then y = 0 when the projectile has flown "t" time. Or in other words, the projectile hits ground (y = 0) after time (t) has passed. So you can insert y as 0 and your chosen t to the function.
From this formula you eventually get:
Vy = gt/2 - h/t.
If your projectiles are thrown "up" or towards the top of the layout you need to take the opposite of this function since in Construct that is negative speed (y is decreasing while traveling to that direction), so we use:
Vy = -(gt/2 - h/t).
I actually improved my example. In this version you can also choose to manipulate Vx since I realized that might usually be more useful that using t as a constant. Remember you could also calculate the time of flight or Vx based on the distance between the player and enemy or any other factor you want, which will give you more tools to tweak the trajectory just the way you want it.