Yeah, that's what I did. You can put the tokens in bags and then tuck them underneath the plastic molds holding the heroes and the cards. However, I recommend doing yourself favor and picking up a Plano box for all of the tokens, dice, and bases. It saves so much time setting up and putting away the game.
^ this. The "insert" for this game was a joke. Almost everyone has done one of three things. They either just store the tokens in plastic bags, use a small Plano tray to hold everything, or built their own insert out of foamcore to hold everything nearly. I will have to do a video on my setup sometime and it holds everything from the base game perfectly. Sadly when you add in the stuff from Beyond the grave, the box now sits about 1/4" higher because of the extra 3 map tiles, but everything still fits. I might even be able to compensate for the extra tiles if I really wanted to mess around with the design.