It is a good idea to have either a "nut hole" or some sort of relief in the important area of the seat.
However, even with a good seat, your butt will be a bit sore for a bit. Get back on, grit your teeth, and deal with the pain for a couple days. If it doesn't get better after a couple days, I'd say you need a different seat.
It does seem strange that you get sore after only a couple miles. It should take more than that unless the seat really just plain sucks.
Bigger is not better. Neither is gel. I've tried (for a very short while) a couple, gel seats and although softer at first, I got butt burn from them.
EDIT: I can't comment on Big Kahuna's gel recommendations. They may be better. I was referring to the bigger "ultra-glide" sized gel seats. I used them on my stationary bike a few years ago. The ones Big Kahuna recommended may be a decent option, especially the knock-off as long as it is shaped properly.
The most important part is that your weight rests on the proper areas of the seat. Unfortunately, sitting on a seat mounted to a bike at the store only gives you a general idea. You don't really find out until you ride.
I have a race saddle that looks like it would be uncomfortable, but the fit is right and I wear bike shorts in addition which helps some as well.
I'll still get sore after 4-5 hours in the saddle, but I figure that is good enough for me.
