Muzzy, first, it will be impossible to get your arrow to run center with the burger button hole on the Bowtech. I've been using the Whammy rests now for the last three years and have triedall three generation launcher arms to get the arrow to run center and it will not happen.
You DO NOT want the launcher arms coming into contact with the riser shelf as it drops away. So for this reason you have to raise the rest higher and this will cause your arrow to line up above the burger hole.
This will not affect the flight of your arrow once you've taken the time to tune the bow.
Start by setting the arrow to string angle at 90 degrees. Make absolutely certain that your launcher arms when depressed have at least 1/16" gap away from the shelf, otherwise the arms will bounce back prematurely and make contact with the vanes. You will need to run a powder test to check for proper vane clearance.
As for serving the cord, at full draw have someone mark your 'up' cable about 1-1/2" to 1-3/4" below your cable guard.
Use this mark for serving your cord and serve towards the "bottom cam" from that point. DO NOT serve up towards the rest.
Insert the allen key (provided with the rest) into the hole ofthe trigger and snug the cord so that the bottom of the trigger hole lines up with the top of the rest block.
Examine that the cord does not turn into the path of the vanes at full draw...if this happens loosen the allen nut on the trigger (reinstall the allen key into the trigger hole and depress the trigger) thenrotate the cord 180 degrees, snug the cord up againand again check to confirm there is cord clearance away from the vane.
You'll need to do this everytime you make vertical adjustments to the rest, hopefully, you'll only need to do this once or twice.
You can start by setting the windage for center shot, but most times you will have to adjust left or right of center to achieve a good paper tear. This willdepend on your arrow spine, the BH weight, cam alignment, tiller balance, bow torque, string creep etc.
You will also need to use the tamers on the launcher arms, otherwise you'll'hear' the drag of the arrow while moving to full draw.
Of course arrow friction on the tamers will take its toll and depending on how often you shoot, the tamers will quite quickly need replacing.
When tuned properly the Whammy works really well.

Shoot with cocked vane 'up'.