You don't actually have these square roots there. The line of thought is like this: $$\frac{x^2}{a^2}+\frac{y^2}{b^2}=1 \iff \left(\frac{x}{a}\right)^2 + \left(\frac{y}{b}\right)^2 = 1,$$so making a change of coordinates $\overline{x} = x/a$ and $\overline{y} = y/b$, we have that this equation reads $\overline{x}^2+\overline{y}^2 = 1$. That ellipse in the $xy$ plane is a circle in the $\overline{x}\overline{y}$ plane, with the axes stretched. We can parametrize it as ${\overline{x}} = \cos t$, $\overline{y}= \sin t$. Going back to the $xy$ coordinates we obtain $x = a \cos t$ and $y = b \sin t$.