If I say "what are you doing now" it means : "have you something planned now "but if I say " What do we do now" could it mean the same thing or as it is present simple does it mean that we are doing something we do regularly
What are you doing now? = What activity are you engaging in now?
What do we do now? = Is a question asking for a course of action.
Possible answers can be given using the same tense.
Imagine this situation: Perry: Oh boy, having our wallets and luggage stolen is the worst thing that could have happened to us on this trip, John. What do we do now?
John: We go to the police station and report it. Otherwise, our travel insurance won't work and we'll really be in trouble.
The use of the simple present is "asking for a course of action" in a specific situation.
Other common questions in the present simple for this type for situation are: - What do we tell them? - Where do we go now? - How do we deal with this? - When do we respond to this threat?
No, they don't mean the same thing at all. With what are you doing now?, you're literally asking the person you're talking to what kind of activity they are in the process of doing as you ask them this question (that is, at the moment of speaking).
What do we do now?, on the other hand, is a question where you're asking yourself and your buddies what should your course of action be or how should you proceed with the current situation. So, as you can see, the meaning is completely different. Notice that although you're using the simple present tense, you're referring to things that will happen in the future.
The upshot of all this is that tense-related grammar does not always coincide with the actual grammatical tense of something. When you're talking about things that will happen in the future, it does not necessarily mean that you have to use grammatical structures that are specifically related to the future tense. This is in general very common in English. For example, future events in English can be expressed using present-tense grammar:
I'm going to Paris next week. (this is what you're actually saying: next week I will be visiting to Paris)
You can try and kill me, but still, I'm not telling anything! (this is what you're actually saying: I won't tell you anything)