Correct, but the former (separate folders) is better, because isClient and isServer code is still sent to both client and server. Using separate folders keeps the code where it belongs. Use isClient and isServer sparingly and only when you can’t avoid it. Don’t put sensitive code in an isServer block thinking it won’t get sent to the client - it will.
It’s also better to split your app into several, related files organized by directory structure - check the Meteor Guide for more information.
You should also look at using ES2015 modules and structuring your codebase according to common patterns - again, check the Meteor Guide and tutorials for more information.