Your question is an excellent one, and your confusion is shared by many women.
Whenever you find a stain, you should refrain from relations for 24 hours to ensure it does not turn into a flow. (Please note that this is a recommendation and not an absolute requirement.) At this time you are not niddah and may engage in any other physical activity (hugging, kissing, cuddling) – similar to your yom haveset.
If the spotting turns into a flow that requires use of a sanitary napkin or tampon, you are niddah, and must refrain from all physical contact.
Your vesatot should be calculated from the day you became niddah, which in the case you described is the day the flow began. Should this happen three months in a row, a specific sheelah should be asked if this can or should be considered a veset haguf.
As far as counting the five day minimum: When one refrains for an entire Hebrew day from relations for halachic reasons, one can count that day towards the five day minimum. However, when one does so simply to be one the safe side, it does not. Therefore, in the type of case outlined in your question, the five day minimum should begin from the day you consider yourself niddah either due to a flow or a stain that does not fit the caveats of stains. See our article on beginning the five-day minimum for more details.