The idea is that if the alleged rapist could not have reasonably believed that the person had consented, then it is rape. So if your partner doesn't specifically verbally say ''yes, sex me'', but seems happy about it and actively takes part, then of course you can reasonably believe that they want to have sex. But quite often in a rape, the victim just sort of freezes up - an understandable response to shocking behaviour from someone they might be scared of - and doesn't specifically say yes or no, but also doesn't really participate in what happens. In such a situation it's really important to make sure that the other person genuinely wants to have sex, or you might be raping them.
To respond to your scenario: in that case, it's completely obvious that they have consented because they have initiated sex, so I have no worries on that front. If I wanted to show that I consented, I would simply have sex with the person, actively, and that would be a form of nonverbal consent. If I didn't want to have sex, I would break contact, move away from them, and say clearly something like ''Sorry, I don't want to have sex'' or simply ''No thanks''.