Stained Hull Question

I stained my CLC 17LT hull light blue.  I just realized that i may have a colour issue when i fillet the hull.  Can i use the same waterbased stain to 'colour' a bit of wood flour for the fillets?  OR am i better off just to cover the seams with graphite when the time comes ( i plan to do this on the keel line anyway...).

 

thanks in advance for all your help! 

fyi i am using the graphite route…i did not have any luck trying to match the fillet color in my tests.