This is a fairly simple process. Just make sure to avoid cutting or ripping the stock seat cover as you remove the staples that secure it to the seat pan. In most cases you can save a lot of time and money by reusing the seat cover. This will be more difficult if you accidentally put a bunch of holes or tears in it.
Remove the seat and check out how much seat cover you'll have to work with in the areas that you'll be modifying. Most modifications will focus on the drivers seat platform. Remember, the stock seat covers can be stretched, so you'll have a bit more to work with than may initially appear.
As you can see, the seat cover is attached using 1/2" or 3/8" crown, 1/4" long staples. Using your tack/staple remover, remove all the staples in the area you'll be modifying, if it's a one-piece seat as shown in the picture. If your working on the driver's seat of a two-piece seat, you'll have to remove all the staples so that you can completely remove the cover.
Be careful not to rip the seat cover under the staples with the tack puller as you pry them loose. Just get the tip of the tack puller under the staple a bit, and then pry it up by twisting it a bit. Don't try to jam the tack puller completely under the staple and then pry; you'll likely rip the cover sometimes doing this.
Do yourself, along with the people and pets you live with... and gather up the staples and throw them in the trash. Getting staples stuck in your feet (or paws) is a pain. If you have a wife, definitely make sure you do this.
After you remove the staples, take off the cover or pull it back far enough to give you plenty of room to work on the area that you want to modify. If you don't give yourself enough room, you can accidentally nick the cover with the grinder when shaping the foam. Then there is a hole in the cover, which sucks.
Here to go... consider this your canvas. On it you'll create your masterpiece! This picture shows a seat attached to the bike, though you'll do most of your work while the seat is removed. Notice how the stock cover is pulled back sufficiently beyond the seat "rise" to keep it out of the way.