luggage toruble and reservation of seats

i will be landing at haneda in first week of july and then which train should i take to tokyo city near ginza district, also i have three big sized suitcases with me.
i will be staying in the city for a week during which will also travel to hakone, so can i use the japan pass in the city as well as to hakone, for hakone, mt fuji , do i have to reserve me seats in advance, if so how do i do that, can i do that before entering japan?
from tokyo i will travel to osaka on a weekday, so will taking a morning train be a crowded/ peak time, also will i be able to take my luggage with me or have to send separately, and which train would i have to take.
also i want to travel to kyoto and nara from osaka, can i use the jr pass for that and which trains would those be, and also the trains in between different tourists spots be also included.
also in osaka to the kansai airport can i use the jr pass?