We can rewrite these two equations $$ F_{x}=-\frac{GM_{\odot}M_E}{r^2}\cos{(\theta)}=-\frac{GM_{\odot}M_E}{r^3}x, $$ and $$ F_{y}=-\frac{GM_{\odot}M_E}{r^2}\sin{(\theta)}=-\frac{GM_{\odot}M_E}{r^3}y, $$ as four first-order coupled differential equations $$ \frac{dv_x}{dt}=-\frac{GM_{\odot}}{r^3}x, $$ $$ \frac{dx}{dt}=v_x, $$ $$ \frac{dv_y}{dt}=-\frac{GM_{\odot}}{r^3}y, $$ $$ \frac{dy}{dt}=v_y. $$