My new toilet flange bolts came with little plastic dealies to keep the bolt sticking straight up while the toilet is lowered. They helped, but it was still nice to have a second person there guiding the toilet down.
If you're just having trouble lining up the bolts with the holes in the bottom of the toilet, then slip a soda straw over each bolt. Then, get a helper to reach under and help align the straws with the holes, as you lower the toilet down. Make sure to remove the old wax ring and put a new wax ring between the toilet and flange.
Paintdrying has it right, but use Jam nuts, the low profile ones. Also use all Brass 5/16 Bolts Locate with a straightedge parallel to the wall, bisecting the pipe. Take the tank off and locate the bowl first, Much easier, and you should be replacing the tank bolts anyhoo. Make sure you put the plastic retainer washers with the lip up, under a stainless flat washer. That lip retains the snap on plastic cover dome.
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