Does this effect only work temporary? It seems that my script works, but when I save my game, exit and then come back, the spells are reset to default.

Will I need to run the code once at the beginning of each game to reset the magnitude to what I want?

That's because on game load, the engine reads from the active mods. Any changes you may have made in your previous game session would therefore get overwritten.

Ok so I'll have to figure out a way to run the spell update code once each time I start the mod.

Use a getGameLoaded block in your script(s) to do the initialization.