I've never done it, but I'm pretty sure it's something like this:
If you open a magic effect, and look at it's "visual effects", those point to art objects. You can open the art object (under miscellaneous in the object window), and see what nif it points to in the "Model" field.
Extract those nifs from the meshes bsa, and open them with nifskope. Find the textures they point to (probably in textures.bsa) and extract those as well.
Once you have all of those extracted, make copies of both the nif and the texture and change the color of the copied texture with photoshop or gimp or something. Then set the texture path in the copied nif to the edited texture file.
Then create a new art object in the creation kit, and set the model path to the new nif you made, and then set that for your spell effect.
The process is about the same for explosions and projectiles, and for many spell effects you may have to change those too. For example, if you just change the "fire" casting art to be blue, you'll look like you cast a blue fireball but the actual projectile will still be orange. So you have to copy and edit the casting art, projectile, and explosion textures if you want it to be consistent.