How do you set negative integer values?

So I'm beginning to make a good map finally, thanks mosly to Vexorian and his CS system. However, I thought his Item system was far too complex for what I wanted. Namely, all I wanted was items that equip and certain sets of them that grant you additional abilites. Anyways, I set out to write my own, and so far it has been great! The only issue I'm having, is that when creating my 2s compliment system, I can't figure out how to set the integer values of say, a damage bonus item ability, or a movement bonus item ability to a negative value. In other words, I can't create a 2s compliment system at all.
I know it's possible, for in Vexorian's InvX 1.8 there are abilities with negative integers, but I don't know how its done. So...

How do you set negative integer values?

Preferences, I think, allow negative values. You can also use shift-enter and then entering the value (this will force any value).

You can't have negatives in some though (such as stat bonuses).

Ya I knew about the Preferences thing, but I guess I'm still a noob, because I've never heard of the Shift+Enter thing. So thanks a lot!

Note: Harded Skin and some other skills crash the game or behave really odd.
Note: Negative state bonuses are allowed, thats why bonus mod works.