for the distinct bolt on flare look use flare rubber strip, its usually black but i think you can get it in some colours now.
you could probably find a rubber seal strip to suit if you can't find the flare stuff.
for the integrated look you can bog or use a flexible paintable filler on the join and over the holes as well if you like but it difficult to
ever remove the flares if you had to (eg accident / cracked flare / rust repair) and it has to be prepped well for paint.
word of warning, don't go the style of forming flares of bog or fibreglass on top of your flares though, it is very hard to get
right and turns into an expensive ugly heavy mess as far as i have seen, not that it can't be done though.
or use a coloured flexible filler matched somewhere near your paint color, not sure if it would last against the elements
but some types may.