I like to bet roughly 2/3 of the pot myself, but that depends on certin factors. Does said opponent hang on to fd's like grim death? If so, smaller bets will do because if they're gonna call you anyways, why give them a big pot if they hit? IMO on lower limits especially, players greatly over value the strength of a fd, and thus are less likely to fold unless given a damn good reason to do so. Sometimes against these players, a massive overbet (pot + 1/2) will be the only thing that will shake them.
Now, on the other hand, if they are a seemingly competent player, I try to give them bad odds. Say the pot is 700, and I figure them for the nut/near nut fd, I would like to bet enough to discourage them calling, yet not too much that they can see I'm trying to discourage a call. Into this pot, I'd say roughly 500.
Though this is all apeculation, of course, and situations vary. I guess it all comes down to what you know or don't know of your opponent, the type of game (ring, tourney), how close you are to the payouts, ect.
Now as far as players re-popping you, depending on the texture of the flop, it's usually fairly easy to define their range. If you feel they are popping on a fd, I find that a smooth call is a bad idea. If the flush card comes, you have no moves, and if it doesn't, they still have the lead on the pot due to the re-raise and therefore can be representing any number of hands that will have your overpair/tp beat and will make it difficult to play with any type of certainty on firther streets. I personally will come back over the top with all my chips, if I feel they are on a fd, and not some type of two pair/trips hand.