In evaluating the size of stains on a garment, we treat each stain separately. (In contrast, stains found on skin are evaluated more stringently, by their total area.) In cases such as yours, where no single stain is the size of a gris, the stains do not make you niddah or invalidate your clean days. You may continue counting your clean days.
Changing underwear with greater frequency can be an effective precaution against larger stains accumulating.
Note that red stains on a bedikah cloth can make a woman niddah whatever their size.