You can't have a negative effect size, it is a physical impossibility. It would mean that there was less than no difference between groups which can not happen. One group could be less or higher than the other and depending on which group you make the reference group the sign of the effect might show as plus or minus - but the effect size is the absolute value of what you find. In other words the effect is the difference between one group and the other.
If A has a mean of 5 and B of 2 then you would get a value of 3 or -3 depending on which you subtracted from which. But the effect is 3.