Hi, Clif. I'm a little confused about what you are asking, but for what it's worth, you should have a flange in the floor and the flange is one end of the soil pipe. The flange has slots where T bolts fit. You should roll a long snake-like shape out of plumbers putty and apply it to the bottom outside edge of the toilet and install the T-bolts in the soil pipe flange. Then you install the wax ring and then set the toilet with the wax ring leading to the soil pipe. It should be set directly on the floor with no carpet under it. Then sit on the toilet to seat the wax ring and the plumbers putty and, finally, install nuts and washers to hold the toilet in place. This process is important to assure that you have no present or future leaks of "used" water from the toilet. Leaks in this area can ruin your floor and carpet, so it is important that it be done correctly.
After the toilet itself is installed, you can connect the flush valve and water.