Most is a superlative, meaning that it describes the highest amount or quality of something. For example:
"Our team won the most baseball games this season."
"I'm the most intelligent person ever."
Many simply refers to a large quantity of things, without any comparison. For example:
"I have many friends."
It doesn't imply that you have more friends than someone else (comparative) or more friends than everyone else (superlative). It just means that you have a lot of friends.