How do you make one box of hair dye cover long hair?

By doing your roots and mixing in a little water into the dye. Not going to get good results, though. Use two boxes for the first application and when you do your roots, in a few weeks, just use one box. If you covered the application well then it should be ok colour-wise.

Alternatively, don't dye the underlayers of hair.

it's probably not even noticeable, and saves dye. Multitonal hair colour looks good.