I'm doing the same thing. First a repo is setup in GitHub using the GitHub provider, when that is done, the base configuration for Flux is added in there and then the lifecycle on that is going to ignore future changes.
Next, an AWS account is generated and then a CIDR is read from Netbox. That is used to create the VPC and subnets, and after that an EKS cluster is created. Next the Kubernetes provider is used to install everything needed for Flux, and it is pointed to the GitHub repo that was setup earlier.
At this point the team that wanted a dedicated Kubernetes cluster can just put their charts and manifests in the github repo and it is automatically deployed.