To use Flume, you do not need to edit the flume.conf file. The better way to write a Flume agent is to create your own Flume config file (and save it in whatever folder you like). Then when you start the Flume agent you point it to your config file with the -f flag; for example:
flume-ng agent -n my_agent_name -c conf -f my_flume_agent.conf