Let's say we have a ball and we dropped it from height $20 \;\text{m}$
Case 1: Taking downward direction as positive
$$v^2 = u^2+2as$$
$$
v^2 = 0 + (2)(10)(20)
$$
$$ v = 20 \;\text{m/s}$$
Nothing wrong until now but check this out.
Case 2: Taking upward direction as positive
$$(-v^2) = u^2+2(-10)(-20)$$
$$v^2 = 0 +400$$
$$v = +20 \;\text{m/s}$$
How can $v$ be positive when we assumed downward direction as negative? Am I misinterpreting something wrong?