I made a little ilustrated tutorial with screenshots, it should be easier for anybody who wants to know how to recolor a FX. My OS is in spanish, so sorry for that. This is the way that worked for me:
1. Open NIF with Nifskope
2. Search for textures in block details. Right-click --> Texture --> Choose
3. Search for the texture in explorer window
4. Right-click-->Open with-->Paint.net
5. Open hue and saturation tool in the adjustments menu (ctrl+shift+u)
5. Move the hue control to the color you like
6. Save it (with another name, you can add just a number or a letter to make it easier to find; Remember to save it as a TGA if it has transparencies, otherwise the transparencies won't work in

)
7. Select the new texture in nifskope (if you kept nifskope open during the recoloring, is faster to just go back to the previous select texture window)
9. See how the nif looks in the preview window
8. If you're satisfied, save the nif
10. Now you need to add the new FX to the game in FFEdit (This is a whole other process that i can explain later

)