Anytime you involve China it can be bad. Beijing and Shanghai, at one point, held the dubious distinction of being the worse in the world for on-time performance. You may find yourself sprinting around to catch your connection.

Japan Airlines operates out of Terminal 3 so there will be a terminal transfer to complete. You'll need to take the connection shuttle between terminals but it runs fairly often unless you arrive in the wee hours of the night/early early morning.

It has been some time since I made a connection there. My mother went through earlier this year and said signage is good. PEK has a transfer guide on their website that may help. There is a brief English video guide (after the Chinese commercials) available on their website. en [dot] bcia [dot] com [dot] cn/ guide/ transfer_i_i [dot] shtml

FT won't allow me to post websites as I don't come out of my lurking to post enough. Insert appropriate punctuation and delete the spaces.

Even though you bought the ticket together, if you went through an agency, make sure it is the same ticket number and they did not present it to you as 1 ticket and then they booked it as 2. Given it's AA to JL, I doubt it since they are both oneWorld. If it's the same ticket (on the same ticket number) then AA will rebook to the next flight to TYO if it is their fault for free. If you meandered into Duty Free/Food Court/Bathroom/fell asleep/got distracted and missed your flight, it's your fault. Keep in mind in the worse case scenario, the next available flight may be to Tokyo Narita rather than Tokyo Haneda but you can connect between the two airports easily.

Most importantly, don't be afraid to ask for directions!