Code obfuscation is typically done when you release your game to the public. During the normal development time, you never want to obfuscate your code.
Which means that you have to get into habit handling multiple development environments (e.g. Release vs. Debug, development - alpha - beta - production). Your code has to cope with those differences in the env too. During development, you output as much as debugging info as possible, turn on fps, wireframe, collision boxes, etc. When you toggle your build to Release, all of that is turned off and obfuscation is turned on.
You still have to retest your game in Release mode as it's now a different binary. There could potentially bugs that arise only when you have it on Release mode.