A-Train HX doesn't have one particular goal or ending, but the first thing you can try is to get to 1 trillion yen (there's a surprise waiting for you when you do). You can also try to get the game's many Achievements (building a bullet train, etc) to increase your Gamerscore.
If your funds reach 0, it's game over. You won't be able to continue with that particular game. To avoid this, be sure to keep an eye on your finances. If it looks like you may run out of money, you can try borrowing from a bank.
No. Downloaded maps and the maps that are included with the game from the beginning can only be used to start new games. You can save your game while playing them, however.