When counting your stocks and doing a physical inventory in SAP MI01 is your starting point. The first step of a physical inventory is creating a physical inventory document, which is done via MI01.
In SAP MB52 is the standard transaction that you will be using for checking your warehouse stocks. There are other transactions that list stocks, but MB52 is by far the most useful.
In SAP MMBE shows your stocks of a material by company code, plant, storage location and batch in drill-down form.
When searching for materials movement history in SAP MB51 is the transaction you are going to use. It is a flexible and neat report that you will find very useful.
In logistic side of operations, most transaction creates goods movement in SAP. Most common SAP movement types from logistics perspective are listed in this article. Being informed about these is very important for tracking...