Simply show your pass (and tickets if taking a shinkansen) to JR officers stationed near the ticket turnstiles and they’ll wave you through.
Shinkansen trains do not have luggage racks for large suitcases. Carry-on luggage can be stored in racks above your seat.
These smart cards work more or less like debit cards that are preloaded with cash and can be used on trains and buses in place of tickets.
Tokyo Station is confusing. I still say this even after navigating the station across multiple trips over the last 15 years.