Thank you for reaching out to us.
One aspect of observing an onah is performing a bedikah on it. This is because the onah is a day or night on which we assume that niddah bleeding is more likely to begin. By performing a bedikah, we check whether that halachic assumption is well founded, and we establish whether we need observe the same onah in the future. This is true for each onah individually. Therefore, you should perform a bedikah on each of the three onot.
The connection between the bedikah and relations is specific to onah beinonit, because the halachic presumption that a woman experienced niddah bleeding on her onah beinonit is stronger than on her other onot. When a woman misses performing a bedikah on her onat chodesh or onat haflagah, she is permitted to have relations afterwards (when it isn’t an onah, and if she hasn’t yet become niddah). If a woman misses a bedikah on the onah beinonit, however, then relations are prohibited until she performs one.
On a final note, there are different traditions for how to calculate the onat haflagah and we want to confirm which method you are using. The configuration that you describe would seem to align with a specific method associated with Chabad. Chabad counts each day and night distinctly in calculating the interval (haflagah). Other traditions calculate the interval based on the halachic dates, and observe either day or night based on whether a woman’s most recent period began during the day or night. (Using a standard non-Chabad calculation, your onat haflagah would be in the daytime like your other onot. See more about standard haflagah calculations here.)
Please be in touch with any further questions.