In general it’s closer to enter through the Yaesu side (where the Daimaru dept. store is) if your are going to take Shinkansen. Tokyo station is big but the signage is quite good so you don’t really need to worry much. Don’t be panic if your hotel is closer to the Marunouchi side. Just enter from there and there will be clear signs to point you to the Shinkansen gates. It will just be a longer walk.