I'm in the process of modifying a weapon mod that has some pretty killer stats and enchantments but I'd like to balance it a bit by making it sap your health and magicka, is there a way to do that?

Sure. Find you weapon in the Creation Kit, and open it up. Take a look at what Enchantment it has in the Enchantment dropdown box. Then you'll need to search for that Enchantment. Once you've found it, open it up, and you can change, add, or remove effects from it.

You might want to look through some tutorials or browse the CK Wiki a bit to learn more about Weapons and Enchantments. http://www.creationkit.com/Customizing_Weapons_%26_Armor looks like it might be helpful to you.