GitLab doesn't provide an uninstall option, so you will either have to manually re-install cert-manager in the gitlab-managed-apps or re-attach your cluster to your GitLab project. If you want to manually do that, run:

helm install \
    --name cert-manager \
    --namespace gitlab-managed-apps \
    stable/cert-manager

That only takes care of the cert-manager part. Another thing to note is that cert-manager doesn't miraculously recognize your need for a certificate and create one. You will need to create required resources such as an ingress, clusterIssuer and a certificate resource. Also one thing to note is that you can use a single tls wildcard certificate for all of your sub-domains. Do not generate redundant certificates, it will take a toll on your quota. Try with the following simple template (eg assuming you are using route53 for your dns provider):

issuer.yaml

apiVersion: certmanager.k8s.io/v1alpha1
kind: ClusterIssuer
metadata:
  name: letsencrypt-staging
  namespace: default
spec:
  acme:
    server: https://acme-staging-v02.api.letsencrypt.org/directory
    email: <your email>
    privateKeySecretRef:
      name: letsencrypt-staging
    dns01:
      providers:
      - name: route53
        route53:
          region: us-east-1
          accessKeyID: <access key id>
          secretAccessKeySecretRef:
            name: <secret name>
            key: secret-access-key

ingress.yaml

apiVersion: extensions/v1beta1
kind: Ingress
metadata:
  name: <ingress name>
  annotations:
    kubernetes.io/ingress.class: nginx
    kubernetes.io/tls-acme: "true"
    certmanager.k8s.io/cluster-issuer: letsencrypt-staging
spec:
  tls:
  - hosts:
    - "*.example.com"
    secretName: cert-wildcard-secret
  rules:
  - host: "sub.example.com"
    http:
      paths:
      - path: /
        backend:
          serviceName: <service name>
          servicePort: <port number>

certificate.yaml

apiVersion: certmanager.k8s.io/v1alpha1
kind: Certificate
metadata:
  name: cert-wildcard
spec:
  secretName: cert-wildcard-secret
  issuerRef:
    name: letsencrypt-staging
    kind: ClusterIssuer
  dnsNames:
  - '*.example.com'
  acme:
    config:
    - dns01:
        provider: route53
      domains:
      - '*.example.com'

Once you have verified that this works (with the FAKE staging certificates) change the URL in your issuer to https://acme-v02.api.letsencrypt.org/directory so that you can create legitimate certificates. Once you've made the change, delete the old FAKE cert secret so the new one can replace it.