ArgoCD together after helm upgrade application?

I am new to GitOps, I have watched some tutorials about ArgoCD, but the applications are mostly deployed by syncing from the GitRepo manifest.

I know that by running the cmd "argocd sync", it will do a pull from a git repo and perform like a kubectl apply -f $FILE.yml

So I'm a bit of lost, My question is that if my old way is to deploy the application via helm upgrade, now I should get rid of helm upgrade cmd to install new app right? Can I still stick to helm and perform some kind of helm upgrade but only generate the manifests and then push them to the git repo that stores the manifest so that ArgoCD can sync the manifest?

If I understand you issue correctly there is no need to create yaml manifest from helm chart and then use it with ArgoCD.

ArgoCD support few template engines (raw yaml, helm, jsonnet and kustomize) and you can directly pass your helm values.

Here is some example manifest:

apiVersion: argoproj.io/v1alpha1
kind: Application
metadata:
  name: gitea
  namespace: argocd
  finalizers:
  - resources-finalizer.argocd.argoproj.io
spec:
  destination:
    namespace: 'gitea'
    server: 'https://kubernetes.default.svc'
  project: apps
  syncPolicy:
    automated:
      prune: true
      selfHeal: true
    syncOptions:
    - CreateNamespace=true
    - ApplyOutOfSyncOnly=true
    - PruneLast=true
  source:
    path: gitea
    repoURL: https://github.com/test/helm-charts.git
    targetRevision: HEAD
    helm:
      values: |-
# Here you can pass all values to overwrite default chart values
        ingress:
          enabled: true
          annotations:
            kubernetes.io/ingress.class: nginx
          hosts:
            - host: gitea.test.com
              paths:
                - path: /
                  pathType: Prefix
          tls:
          - hosts:
            - gitea.test.com
            secretName: tls-wildcard-test-com
        resources:
          limits:
            cpu: 600m
            memory: 600Mi
          requests:
            cpu: 500m
            memory: 500Mi

Here is also documentation describing more ways how to integrate ArgoCD with helm.