As with anything, the answer to this question is "depends."
Each company has a slightly different way of doing it. I'm most familiar with
Alamo, National, and Thrifty, since I've been booking with them for the last few years.
Alamo and National both tell you the full, undiscounted rate on the screen where you select your car class. Then, on the next page, they show you the full rate, subtract the discount and any coupon you might have entered, add all of the taxes, franchise fees, recovery fees, etc., and give you an estimated grand total. My actual total for an Alamo or National Rental has never varies more than about $2 from the estimated total on my ressie.
Thrifty simply shows the discoutned rate on the car selection page, then applies any coupons you might enter when you get to the total page. Again, the estimated grand total at Thrifty includes an itemized list of the taxes and various fees, and my actual total has never varied more than about $2 from the estimated total.