To use the boss flag

that depends on where they are.
example....
to get the town to change after beating a level you build several towns exactly alike except for different strings or whatever else you want to change in town, and then put a warp in line to take you to it from a transition screen, like the screen entering the town.
In short, you have the warp take you to identical but different screens displaying the new "string"

Where would you use the boss flags and how do they affect the warps?

ok....
you set a boss flag in the boss room of level 1 and you want the town to change after beating level 1...
SO you make a screen leading to town and you place a direct warp in secret combo 16, set the boss flag on that screen, set a trigger enemy on that screen, place the flag 16 on the ground where link can't miss it, cover that spot with the ground tile on layer 1 or make the warp tile match the ground so it won't show when triggered, and set "no secret sounds" on that screen, and enemy = secrets.
That warp then sends the player to a screen you've made that is identical, so he can't tell he was even warped.
The level numbers on the dmaps have to match, so the level 1 and the town screen will both be marked level 1 on their dmaps.

What if I want just a house with a guy to change?

The same thing, or different?

If you want the guy to change, the guy would have had to have been a regular graphic on a layer for it to change.

You could also set up a warp similar to the one Freedom described, put two rooms in the guy's house, and put the warps in the first room so that you warped to a new, identical house with a different screen once the boss flags triggered. Then you would only need to copy the house rooms instead of a whole village.

BH4,
He wants the string to change, so he would have to use dupe screens.

The house itself wouldn't have to have 2 rooms, you could do the warp leading to the house on the overworld, so you would actually be entering a different house, but remember only 1 tile warp per screen, so build to compensate for that.

Thanks you guys. I really apreciate your help.

The enemy->trigger: does this have to be placed anywhere specific?

It can be put anywhere on the screen.

TIP:I say putting it around a Corner is better as it will be less disturbing
Afterall its not a combo(The one like a burn flag where you burn trees with candle)