Mazal tov on the birth of your baby!
Many women do stain on the progesterone-only pill, especially during the first few cycles of use. Therefore, there is an advantage to starting the pill after you immerse. At that point, you can wear colored underwear, avoid looking at toilet paper, and take other precautions connected with the halachot of staining. (Please see our articles on staining and toilet paper for more information.)
The disadvantage is that you will not be protected from pregnancy at this point and would need another contraceptive for a few weeks. In the interim, between immersion and when the pills become effective (usually considered to be about two weeks from starting), you could use spermicide.
Do double check with your physician that this would be acceptable. Note that the use of condoms for this purpose is not halachically acceptable. The diaphragm is also halachically acceptable, but spermicide would be easier if it suffices. If you are exclusively breastfeeding, your chances of becoming pregnant at this stage are quite low; please see our article on the Lactational Amenorrhea Method of contraception for more details.