so should i ever put anything in the arduino folder or always use the arduino folder in the documents folder?
It's easier to understand and answer this question if you follow the Arduino installation guidelines, and use Arduino as the name of the sketch folder, and arduino-xxxx as the name of the version-specific installation directory for the Arduino code.
Then, the question is "so, should I ever put anything in the arduino-xxxx folder...", and the answer is generally no. There are exceptions, as always, but when they arise, you'll know it, you'll know enough to know that it is an exception, and you will be confident enough to do it (and to deal with the situation when you screw things up). For instance, if you are creating a new arduino-ish board, you need to add stuff to the core folder to make that board known to the IDE. Are you likely to do that as a newbie? Not hardly. By the time that you feel that none of the existing Arduino boards exactly fit your needs, you'll know what to add, where, to safely modify the installation.
or always use the arduino folder in the documents folder?
is almost always a better idea.