Saddle height: with one of your feet at the 6 o'clock position, i.e. straight down, there should be a slight bend to your knee.
Reach to handlebars: whatever is comfortable for you. If you want to go fast, the lower the better, in most cases. Stem will be a little longer as well.
For comfort, short horizontal distance with the stem, and higher handlebars.
However, it should be noted that comfort and speed don't have to be mutually exclusive. I am very comfortable on my bike, even though I've been told by others that "That has to be painful" due to the relatively low wind resistance profile I present by stretching out a bit.
Also, why on earth would you want to wear underwear under bike shorts? The point of bike shorts is to replace underwear and provide functional comfort.
There are a ton of things to check... but what I check are the following for a quick setup.
The saddle height is set by putting your heel on the pedal and pedalling down until the crank arm is at the 6 oclock position, like mentioned above. And you do want a slight bend. Using a pendulum helps but isnt necessary. But once you think you've got it set right, go ahead and pedal normally. If you hips rock, you're set too high. Also, for me, my knees pop if I'm too low.
For handlebar length, or cockpit there is a generic way to get a good fit. Once you have the height of the saddle set. Then reach for the hoods on the bars. Relax your elbows and look straight ahead. Drop your eye sight. Look for the front wheel hub. You want the hub to be hidden by the handlebars as close as possible using the line of sight from the eyes - bars- hub. Hope that makes sense.
Once last thing I check is the bar width. I ride a 46. This is necessary to ensure proper breathing and posture.