i ended up thinking that using the Firmata library would be a good option
If you think that turning the arduino into a dumb I/O machine is a good idea then I think you have a lot to learn.
is there a way NOT to create a new file on each time i run the sketch?
Yes, don't create one.
// Create the output file
output = createWriter("potValues.txt");
The comment is the clue.
Is it possible to do something like?......
Yes, try opening the file for read, then read to the end and then add stuff.