Typically if you are using clip on aero bars on a road bike, you slam the saddle forward, then raise it a bit to compensate. The reason being:
Road bikes have a typical seat tube angle of 73 degrees, a TT/Tri bike has an angle something between 76 and 78 degrees, thus it has a shorter top tube than a road bike. If you put aero bars on a road bike then the longer headtube will mean you are reaching too far forward and bending at the waist a lot, this closes the hip angle and negates any aero benefit due to power output reduction.
By pushing the seat forward, you are essentially increasing the effective seat tube angle of your bike, but you are also closer to the bottom bracket height wise, so to preserve proper pedalling motion the seat needs to go up a bit.
The effect you are looking for is to rotate your road possition forward around the hip, not to crunch up in the middle.
In short, unless you are adding clip on aero bars, you should not alter your bike for time trials (assuming your bike is well set up in the 1st place).