(I will assume this connector is a through-hole part.) If you drafted the footprint correctly you need only one footprint. Both top and bottom pads, correctly aligned and oriented, are included in one footprint. Each of the 100 pads on your connector must be specified as “Pad type:” of “Through-hole”, and the affected “Copper Layers” must be “All copper layers”. Each pad’s “Properties” will look something like this in the Footprint Editor:
(I believe “All copper layers” is the default condition when you specify a “Through-hole” pad.)
If you don’t trust a faceless, superannuated, guy to give you reliable advice in this matter, place one of your footprints on a board - plot an output file (Gerber, PDF, Postscript, etc, as you wish) for both F.Cu and B.CU and see if the pads appear on both layers.