Mazal tov on the birth of your child!
We're sorry to hear of your staining difficulties.
Staining is fairly common on the progestin-only pill, which is commonly prescribed to nursing mothers. It may help reduce staining to take the pill at the same time every day. Additionally, you should consult your doctor about taking a half pill every twelve hours. These measures sometimes help because they help maintain an even level of hormones in your body throughout the day.
It is common for staining to last up to two cycles. By that point, most women adjust to the new hormonal environment. Many cease to bleed at all, not even once a month! So we suggest, assuming your doctor agrees, that you try to stay on this pill for one to two more cycles.
It is also very important to bring any stains or bedikah cloths to a rabbi for evaluation, prior to deciding that they are problematic. It may also prove worthwhile to review our article on staining. You may also wish to consult with your rabbi about the possibility of reducing the number of required bedikot until this problem is resolved.