As other commenters have said, I think you should consider hiring a software engineer. It's easy to get overwhelmed by tools and minor details.
It's difficult to give you advice, since you've asked such a general question. I've written some thoughts on the matter, but take it all with a grain of salt. At best, my comments are spherical cows [0].
There's nothing wrong with having everything in a single folder; it really depends on the project. If you find it difficult to navigate your way around the source, I'd say there's two high-level approaches for organizing application code: you either group things by feature or by functionality. For example, many traditional web frameworks group source by functionality, so you have a folder for all models, controllers, views, configs, etc.
When structuring application components, you'll typically want to separate things into pure modules and anything which produces side-effects. Pure modules are typically easier to test and debug. If a module depends on anything, consider passing in any parameters during startup or when calling the module, rather than having it look things up on its own. That's the basic idea behind dependency injection.
Git is pretty much the standard for version control. You can get pretty far by just memorizing a few commands [1] and throwing up your code on Bitbucket, GitHub, or GitLab. To make life easier on yourself and your teammates, I'd suggest using a GUI tool like SourceTree. It makes it much harder to shoot yourself in the foot, while providing a far more approachable and discoverable interface. I'm not the biggest fan of git, but since it's what everyone else uses, you pretty much have to suck it up.
Since I'm not familiarized with the ecosystem I can't give much advice with regards to testing. The closest thing to a standard testing interface that I'm aware of is TAP [2]. I'd highly suggest checking out "An introduction to property based testing" [3]; it's one of the most insightful testing-related talks I've seen.
[0] https://en.wikipedia.org/wiki/Spherical_cow
[1] https://xkcd.com/1597/
[2] https://en.wikipedia.org/wiki/Test_Anything_Protocol
[3] https://fsharpforfunandprofit.com/pbt/