The earlier tip about polyurethane, polysulfide and silicone is absolutley correct.
I found that the best way to rebed a fitting is to remove it completely. Clean the bottom of the fitting and the deck carefully. It is best to use laquer thinner, mineral spirits and some other solvents will leave a residue. Then tape over the entire area with blue painters tape. Place the fitting on over the tape dry with the bolts. Cut the tape around the perimeter with a knife. Remove the fitting and then remove the tape under the fitting. Put the compound that you are using on the bottom of the fitting with the bolts already through it. This will minimize the amount of compound that ends up on the threads of the bolts, the inside of the cabin and yourself. Use rubber gloves when working with either polyurethane or polysulfide and bolt the fitting down. Smear a bead of the compound around the base of the fitting after you have tightened it down. Clean up with the laquer thinner and remove the rest of the tape. Use paper towels to clean up and throw them away immediately.
Be careful when working with the bedding compounds, they have a way of very quickly speading all over your tools, boat, clean up rags, glasses, everything. Maybe I am exceptionally clumsy, but, if I did not work like a surgeon I ended up covered head to toe in the stuff.
Some people use the bedding compound on the underside of the backer plates or washers. I do not believe in this practise. If the fitting is going to leak you should be able to see it leak for two reasons. First, so you can fix it. Second, if the water is not traveling out of the deck it is soaking up you core and rotting it.
Good luck!
