I love it too to use the right tokens.
So getting a seperate token-box seems the best I guess. For very specific tokens as emblems, I do them to the specific deck.
For the most I got that cheap plastic ultimate guard Deckboxes. In the 100+ comander boxes, tokens and sidebaord should be fit in. I do not have that much cEDH.
My playgroup got a folder at the place we play, with almost ALL tokens usually used and even some weird stuff as well.
I use that Bundle Boxes as well for decks and tokens. There should be no problems with space in it.
best