Don't edit .vmoptions and .properties files directly, it will violate the application signature, always make a copy of the files under IDE configuration directory and edit the copy instead.
These are locations for the VM options files:
~/Library/Preferences/<appFolder>/product.vmoptions and system properties from ~/Library/Preferences/<appFolder>/idea.properties, where product states for one of the following options: idea, phpstorm, webstorm, pycharm, rubymine, appcode.
For example, to use -Xmx2048m option you should copy the original .vmoptions file from /Applications/PhpStorm.app/bin/phpstorm.vmoptions to ~/Library/Preferences/WebIDE90/phpstorm.vmoptions, then modify the -Xmx setting.
The final file should look like:
Copying the original file is important, as options are not added, they are replaced.
This way your custom options will be preserved between updates and application files will remain unmodified making signature checker happy.
The original file is located in /Applications/<Product>.app/Contents/bin folder (/Applications/<Product>.app/bin for the older IDE versions).