I did something similar a while ago as a pet project.
Once you start working with wind that is not directly from behind or from the front, you move the system to a 3D system.
Subscripts denote projectile (p), wind (w) and their components (x,y,z).
The first order ODE's for such a system are:
$$ \frac{dx}{dt} = v_{px} $$
$$ \frac{dy}{dt} = v_{py} $$
$$ \frac{dz}{dt} = v_{pz} $$
$$ \frac{dv_{px}}{dt} = a_{px} $$
$$ \frac{dv_{py}}{dt} = a_{py} $$
$$ \frac{dv_{pz}}{dt} = a_{pz} $$
where the acceleration of each component is given by
$$a_{px} = \frac{-0.5 C_d \rho A (v_{px}+v_{wx}) ^ 2}{m}$$
$$a_{py} =\frac{-0.5 C_d \rho A (v_{py}+v_{wy}) ^ 2 }{m} $$
$$a_{pz} = \frac{-0.5 C_d \rho A (v_{pz}+v_{wz}) ^ 2}{m}-g$$
remembering to account for gravity in the z direction
This worked out for me, though I'm not 100% sure I'm handling the wind correctly. Hopefully someone can chime in here if I made a mistake.
For your project, I hope you have a spherical projectile. It gets really ugly, really fast if it is something similar to a bullet. In that case, the moment of the projectile has to come into play as well, extending the problem to a 6 DoF system. Then, the Area of the projectile in contact with the wind changes with the rotation. With a complex shape such a bullet, you'll have to do some nasty surface area calculations to determine the drag.
PS: When simulating this, you need checks to stop the solver once the projectile "hit a target" (for e.g the ground) otherwise the integrators lose their mind. I "overcame" this by using a IF-Then-else statement where the IF condition was that if the target hasn't been reached (with a simple distance calculation), the ODE's will be as I described. Else, all ODE's will equal"0" and thus nothing will be calculated further. There is probably a better way to exit a ode45 in matlab, but I'm not proficient enough to adapt it for my problem.
EDIT1: The drag coefficient also changes with velocity (Reynolds number relationship) but is luckily quite well documented for a sphere. A bullet isn't that well documented, though.