Not all stains render a woman niddah. It is definitely possible that the stain you found did not make you niddah, and if you then checked before intercourse and were clean, you may not have transgressed at all, even though your period began the next morning.
In any case, you certainly are allowed to (and should!) observe the niddah period and taharah process this month. In this situation there is no difference in the process; you should observe the five day minimum from the morning you considered yourself niddah before counting the seven clean days and immersing.
Even if a woman were to transgress and engage in relations during her period or during the clean days, G-d forbid, she should still complete the taharah process. There may be some minor changes, so an individual question should be asked.
Please feel free to get back to us with any further questions.
B'hatzlacha!