the only time I use graphite is with the pack races, which for us says to use graphite and has a rule about having slots and the axel in the slot, as such its not too hard.
Otherwise, my current drilled holes (no slots) are only for NPWDRL races and I use oil for those so that is a non issue.
However, my impression is the only ways would be:
1. Since I try not to glue my axels in anymore (or if I thought it might come loose I only use a small drop of wood glue anyway so its pretty easy to remove the wheel and axel) I can remove, regraphite, and then reinstall.
2. if I couldnt or didnt want to remove the axel and wheel I guess the only way would be to drop/squirt graphite between the wheel and body of car (I agree its tough especially if you leave only 1/32" gap) as best as you can and then tilt the car and tap in the graphite so it falls into the bore, and then do the same on the outside wheel by doing your best to squirt it just under the head of the nail and tap it in and then spin....
I think I read somewhere on other sites about drilling/shaving what amounts to as a small grove on the underside of the car over the axels to allow you to better fit the tip of your graphite squirt bottle into the area between your axel and body but I never really tried that or know how that works, or it applies to slotted or non slotted cars or both.
I cant think of any other way to do it....and its certainly messy!
W