There's no bad way to do this, because the number of files wont harm the system, unless it goes to extreme limits I've had 100's of 1000's of files at some points.

What I did in my latest project is to use a database for information, storing 100 000's entries and communicating through a PHP file (for security) that connects the database and to the application. This is in case you'r going Multiplayer.
Otherwise, dont worry, small text files are OK.

And, it should be possible to change only parts of those files... I didnt really understand what stops you?