I have a two input furnace and I want to say that when itemstack1 isn't Elementum.ironCell OR TileEntityCellingMachine.isItemFuel(itemstack1) // which means all items that power the furnace

put the itemstack1 (which can be any item) into a slot number 0.

 

For some weird reason it won't work.

 

Here's the method:

public ItemStack transferStackInSlot(EntityPlayer player, int slotNum)
{	
ItemStack itemstack = null;
Slot slot = (Slot)this.inventorySlots.get(slotNum);

if(slot != null && slot.getHasStack()){
	ItemStack itemstack1 = slot.getStack();
	itemstack = itemstack1.copy();

	if(slotNum == 3){
		if(!this.mergeItemStack(itemstack1, 4, 40, true))
		{
			return null;
		}

		slot.onSlotChange(itemstack1, itemstack);
	}
	else if(slotNum != 2 && slotNum != 1 && slotNum != 0){
		if(itemstack1.getItem() != Elementum.ironCell || !TileEntityCellingMachine.isItemFuel(itemstack1)){
				if(!this.mergeItemStack(itemstack1, 0, 1, false)){
					return null;
				}
		}
		else if(TileEntityCellingMachine.isItemFuel(itemstack1)){
			if (!this.mergeItemStack(itemstack1, 2, 3, false)){
				return null;
			}
		}
		else if(itemstack1.getItem() == Elementum.ironCell){
			if (!this.mergeItemStack(itemstack1, 1, 2, false)){
				return null;
			}
		}
		else if(slotNum >= 4 && slotNum < 31){
			if(!this.mergeItemStack(itemstack1, 31, 40, false)){
				return null;
			}
		}
		else if(slotNum >= 31 && slotNum > 40 && !this.mergeItemStack(itemstack1, 31, 40, false)){
			if(!this.mergeItemStack(itemstack1, 4, 31, false)){
				return null;
			}
		}
	}
	else if(!this.mergeItemStack(itemstack1, 4, 31, false)){
		return null;
	}
	if(itemstack1.stackSize == 0){
		slot.putStack((ItemStack)null);
	}
	else{
		slot.onSlotChanged();
	}
	if(itemstack1.stackSize == itemstack.stackSize){
		return null;
	}

	slot.onPickupFromSlot(player, itemstack1);
}


return itemstack;
}

Don't need help anymore.

Solved it by myself