You can adjust the buy-in amount when you buy-in each player. So even if you set the buy-in at $100 in the Buy-in section on the Game tab, when you buy-in the dealer you can change the amount to $50 for that particular buy-in. You do this on the actual buy-in window, not on the Game tab. You leave the amount on the Game tab set at $100, although you could actually do it that way too if you wanted, but I would recommend just adjusting the buy-in amount at time of buy-in.
If you want to get a little fancier you can create a separate buy-in profile for dealers. Press that big + button next to the Buy-in section on the Game tab. Then when you buy-in your players and dealers, you don't have to change the buy-in amount, you just select the appropriate profile.