"Many" is used with items that are countable: "How many dogs?" "How many cars?"
"Much" is used for collective nouns/things that can not be broken into individual units:
How much rain? / How man rain drops?
How much money? / How many dollars?
How much food? / How many sandwiches?
In, at, and on are used in many different situations. There are sometimes small differences in their meanings. There are times when it will seem like on of the words should be a better fit, but a different word is actually correct. You will have to learn them through experience.
In GENERAL: In - "enclosed by". On - "Atop". At - "having the location/time of"
BUT they all have many other meanings also.