I have a 5.5 turkey breast I'm marinating overnight do I judge the cooking time on the original weight of meat or on the weight of it after it comes out of the marinate?
You don't judge cooking time. You measure it with a thermometer and get it out when it is done, as indicated by internal temperature.
All estimates of cooking time based on weight are not precise and will frequently lead to over- or undercooked meat. If you insist on using such an estimate, it doesn't matter much if you use the weight before or after marinating, as your error will be larger than the variability caused by weight difference. Choose whichever weight you want to.
To extend on Rumtsho's comments, for a turkey breast, you probably want to roast it until the internal temperature registered approximately 155-160 F on an instant read thermometer inserted into the deepest part of the breast. When you remove it from the oven and let it rest, the temperature will continue to rise (as heat from the outside, which is hottest, moves towards the center) to about 160-165 F.
This should give you a moist and delicious turkey breast.
The temperature is the key factor, but you can expect at moderate roasting temperatures, to get a cooking time around 2 hours.