Well, what I try to do is create an environment the player can move around in. Like when you're given an option, it's something like "walk down the street" or "go back home". And you can return to places whenever you want, or go somewhere else and advance the story. The trick I use so that you can revisit certain places after you advance the story (so that you can find new events) is by creating a new variable for every separate location. So my variable list looks like:
place 1 = 0 place 2 = 0 place 3 = 0...
And the first time the player enters any given location, the variable increases 1:
place 1 + 1 ...and so forth. This way the player feels like they are in a real environment with dynamic events, rather than a point A to point B VN. The obvious problem is that I end up dealing with a lot of variables. Not a problem for any old PC, but I'm not sure if this is something these DS VN programs can handle (I seriously don't know, my computer knowledge is extremely poor).