Trainer miles are hard. All my seats start to bother me after about 45 minutes on the trainer, even when I can ride for hours on the road with no problems.
That being said, I do use the trainer to adjust my saddle. 45 minutes to an hour on the trainer will let me judge what needs to be changed in height, tilt or for-aft. Change one at a time after each session, minor adjustments, come back the next day and do it again. When you think you've go it close, go for a spin on the road.
Often too much padding is the worst you can do if you have numbness problems, as you sink into the padding creating pressure everywhere, instead of just on your sitbones. Extra thick padding in your shorts can compound the issue.