There are two ways you can do it:
1) Create a Discounts channel, and assign it in CartThrob
2) Create a Coupon Codes channel, and assign it in CartThrob
If you do the former, the discounts are automatically applied to each order.
If you do the latter, the user will have to enter a coupon code on the checkout form in order for the discount to happen.
You'll also need to put the HTML in place for the Coupon code to appear on the checkout form something like this:
<fieldset name="Coupon Code" class="control-group">
<label for="coupon_code" class="clp">Coupon Code</label>
<input id="coupon_code" class="field-bg clp" type="text" name="coupon_code" maxlength="31" />