I bet your bike shop has a riser built specifically for use with the trainer. They are typically made of plastic with an indentation for the wheel to fit into. Some are more elaborate and have indentations for a couple different size wheels. The piece of wood suggested previously works well, too, as does a thick, heavy book. (I use an OLD textbook that is good for nothing anymore.....)
Even if you are accustomed to your saddle and don't have any problems with it riding outside, it can still bother you on the indoor trainer, simply because you just sit and ride, there's very little side to side movement, there's no weight adjustments, there is no leaning or steering, etc, etc. You can stand occasionally while riding. You can try do some rythym moving while riding, but it still may get uncomfortable after awhile. It does improve with time on the trainer. Your nether regions get more accustomed to it. I pretty much just decide that a little discomfort is worth it if it's the only way I can ride. We can suffer for our sport, can't we?
Time is a companion that goes with us on a journey. It reminds us to cherish each moment, because it will never come again. What we leave behind is not as important as how we have lived." Captain Jean Luc Picard