Hi Bill!
John:
If your double relay has a black square, it is the correct version for your year Boxster and you have the "B Version" transmissions and set-up. That also means that you don't have the traditional B-Pillar microswitch and don't have the black lever microswitch. Both of those have been moved to the INSIDE of the driver's side (left side) transmission in the B-version set-up.
If the electric motor is not spinning, apply 12 volts directly to the electric motor. If it does not spin, the motor is faulty or has a dead spot. If it spins but does not spin when you depress the switch, either the switch is faulty, the double relay is defective, or there is a fault/short in the wiring from the switch to the electric motor.
Here is a procedure I previously wrote up for manually lowering the top if it's stuck in the completely closed position (note that there are some symptoms that don't apply to your case, but the procedure is the same):
The easiest way I have found to access the 'works' if the top is stuck in the closed position is to partially and gradually open the top by using a cordless drill. Since you described the power drain and the loud cracking sound, your drive cables are probably intact and thus you can use this method after unlatching the top latch.
First, reach under or through one of the roll bar hoops so that you can grab the thin metal bar that runs from left to right and that is attached to the rearmost edge of the black vinyl apron under the rear bow of the convertible top frame. That long bar (flat metal bar with a 90 degree bend, about 2 1/2 feet long) is attached to the rear firewall in the convertible top well by means of two small plastic brackets or receptacles, one on each side, about 1 foot to each side of center, 8 to 10 inches from the level of the clamshell when it is in the closed position. Reach for one side at a time and twist it off the brackets by turning it down and rotating it towards you. That will free the vinyl apron from the firewall and give you access to the sides of the electric motor.
The electric motor is located exactly in the center of that rear firewall and, in a '97 also has a small lever mounted on the top of it. (Your 2000 will not have this small black lever) You will see the black vinyl sheath of each of the two drive cables going into the sides of the electric motor. There is a brass colored upside down U-shaped clip preventing each cable from being pulled out of the side of the electric motor. The U-shaped clip has a little tiny shelf at its top surface and that is what you should push upwards on to remove the clip. Once you have pushed the clip up and off, grab the cable where it goes into the side of the electric motor and pull it in an outboard direction. Do that on each side.
Once you have pulled the vinyl sheath off, you will see the inner steel (speedometer-type) cable sticking out by about 3/4 of an inch.
Put one of the inner cables into the drill chuck and set the power drill on a LOW TORQUE setting. Now operate the drill while observing the direction of rotation of the V-lever on that side. The V-lever is located just behind the base of the B-pillar, below the level of the top surface of the rear-quarter panel. If you are spinning the drill in the wrong direction, you will hear that loud cracking noise again as the black "hydraulic" pushrod pulls the half-moon gear past its last (50th) tooth and the top will NOT start to open. In that case, spin the drill in the opposite direction and you will see the top start to open slowly (Your B Version transmissions have teeth going all the away around the complete 360 degrees).
Just spin that side for a few seconds, then disconnect the drill from that side and insert the other drive cable into the chuck. Repeat the same procedure as above until the other side of the front edge of the top has reached the same spot at the side you did first. Then go a little further with that side.
Now just repeat, alternating each side and that will allow you to open the top until you get the clamshell in the 45 degree position. That will give you clear access to the electric motor so that you can re-insert the drive cables and then install the U-shaped clips to lock them in.
If for some reason your cables will not spin the V-levers, you will have to unbolt the 19mm Loctited bolt from the center of each V-lever. That will release both front and rear pushrods on each transmission and you can manually operate the canvas top and the clamshell. You can then install your hardtop. Take a look at page 19 of the Part II PDF at this link for a good photo of the 19mm bolts at the center of the V-Levers: https://sites.google.com/site/mikefocke2/installinga'03-'04glasstopandframeona'97
That should do it.
Regards, Maurice.