You can simply ignore the sign of overlap, it is fully arbitrary. Only absolute value has practical value.

I´ve been working on some calculations of organic molecules, trying to obtain the orbital overlap between two fragments. However, for some dimers the overlap is negative (e.g. -0.15 in one case, but for other cases 0.15  and 0.16). What´s the importance of this sign ? Or we just to worry about the absolute value (0.15, 0.15 and 0.16) of the overalp?

Thanks for your help