Have exactly the same problem, blonde roots!
Saw a guy (makeup artist) on youtube suggesting using an eyelash comb to apply mascara rather than the brush, I guess that would work but I haven't managed to get myself a comb yet. Or how about a flat stiff brush to 'push' the mascara on to the lashes?
Most days, not out yet, I use clear mascara to keep the bristles under control, they do appear slightly darker too.