You won’t have to use association, you can use the built-in smartthings features to have one switch mirror another if you would rather do that. That way when the auxiliary switch is turned on, the master switch will follow it and turn on as well, which is what turns on the fixture.
The only reason to use direct association is if you want to be sure that the auxiliary switches will work even if your smartthings hub is not working. So up to you, but actually most people don’t use association. 
So you can stick with just the official features and still set up three-way switches.
If you do want to use association, the Z wave tweaker is certainly as safe as any other custom code provided by another community member. It’s listed publicly, and lots of people are looking at it. And there’s not much it can do anyway.
As far as how to use custom code, essentially you’re just going to copy and paste it into your account. Then assign it to the device you want to have use it. Once you have the association set up, you can assign the device back to the original DTH.
Here’s the FAQ on how to use custom code: ( The topic title is a clickable link)
But again, if it makes you nervous, you don’t have to do that. Just use the official features to have one switch follow the other.