You will want to use Temp = TempRead + 0.25 - (CountPerC-CountRemain)/CountPerC) when the value is negative.
Another recommendation would be to use the formula as shown on page 6 of the DS18S20, but treat the Temp read as an absolute value while you do this calculation. Then change the final calculated value to positive or negative depending on the sign bit. This will give you the same result as the equation above.