Yes the two formulas say the same. $((\exists x)\phi(x))\to((\exists y)\psi(y))$ is equivalent to $(\lnot(\exists x)\phi(x))\lor((\exists y)\psi(y))$ which is equivalent to $((\forall x)\lnot\phi(x))\lor((\exists y)\psi(y))$ which is equivalent to $(\forall x)(\exists y)(\lnot\phi(x)\lor\psi(y))$ which is what you are looking for, namely $(\forall x)(\exists y)(\phi(x)\to\psi(y))$.