For the drain flange, there is no "seal" per se on top of the tub. Silicone or plumbers putty is used as a cushion. Either of these is safe for cultured marble. Putty is definitely not recommended for the poruous natural stone. Silicone generally is the preferred product for natural stone. I don't know what product you have that is not recommended.
The rubber gasket goes under the tub, between tub and shoe.
Post a picture of the assembly so we can see how the overflow looks.