Hershisquirt

I am trying to figure out the proper way of making sure changes to the config are applied to the server. Either the changes are delayed substantially or i am restarting/saving settings wrong. Typically I make a change to a file/s re-upload them to the FTP server then go into the control panel and near bottom where it says save settings and restart server and click that. Also I noticed any edits made directly to the network file then doing this process seems to reset anything that was changed in the network file. Right now my biggest issue is pressing stop, doesn't seem to stop the server. The other is that clearing/cleaning save file doesn't seem to regenerate a new world. What am I missing?