I might just be illiterate about this subject, but I’m a new developer and I’m learning. Hopefully I can be helped with this question of mine, I looked all over online and couldn’t find a thing on this subject! Any assistance would be appriciated! (Examples would be lovely so I can better understand what you may be talking about) Thanks to all who are reading this! 
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You could use folders to manage your game’s stuff. This is great if you have lots of parts and you want to edit only some parts, (Good for when you want to find something quick aswell) 
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Frameworks. A framework will control the flow of the game for you and provide tooling to your scripts so all you’re realistically doing is writing code in one location. There will be virtually no mass structuring changes you need to actually do. A good starting place to go: AeroGameFramework.
Library loaders will decouple systems for you and allow you to reuse in some cases. You will still be expected to maintain such structure using one, but not as much as if you just write your code completely independently. So it’s half the organisation a regular game would call for. Nevermore is a popular resource which is already stocked with many libraries readily available for your own use.
There are a couple of other topics related to game structuring that you can search up on the DevForum. For example, the following thread is all about frameworks and game structuring:
https://devforum.roblox.com/t/advice-for-writing-a-game-framework/42945
You can use as much structure as you want.
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As @HmmBilly and @446576656C6F706572 said, organization is probably the key to this exercise.
Since we can’t foresee what kind of updates you’d plan on putting into the game it would be hard to give you advice on things like this.
Knowing where your stuff is is 95% of the battles most times. If you can’t find it, you can’t fix it!