on the inplanon and the pill?

I had the inplanon for about 6 months which never helped me with pain or regularity or even heavy it would give me 40 day periods with a 5-10 day break then another 20-30 day period and so much blood. I went to the doctor about it and he gave me the pill but never took the rod out he said he needed to check if it was just a hormone imbalance or if i had somerhing wrong and everything is perfect now so i guess its fine but is it ok to keep the rod in and still take the pill? Im fine with it im just scared that if i take the rod out things mught turn to crap again and i shouldnt bother if there is nothing wrong so is it ok or is it not healthy or??? Can someone explain