diff --git a/manifests/v2/base/kustomization.yaml b/manifests/v2/base/kustomization.yaml
deleted file mode 100644
index 43eb72b72e..0000000000
--- a/manifests/v2/base/kustomization.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-apiVersion: kustomize.config.k8s.io/v1beta1
-kind: Kustomization
-# We can't set namespace in the overlays since we use remote JobSet manifests in the resources.
-namespace: kubeflow-system
-resources:
-  - ./crds
-  - ./rbac
-  - ./webhook
-  - ./manager
diff --git a/manifests/v2/base/manager/kustomization.yaml b/manifests/v2/base/manager/kustomization.yaml
index 7394a6d059..a62e9473d9 100644
--- a/manifests/v2/base/manager/kustomization.yaml
+++ b/manifests/v2/base/manager/kustomization.yaml
@@ -1,2 +1,4 @@
 resources:
   - manager.yaml
+# TODO (andreyvelich): Move it to overlays once we copy the JobSet manifests.
+namespace: kubeflow-system
diff --git a/manifests/v2/base/rbac/kustomization.yaml b/manifests/v2/base/rbac/kustomization.yaml
index 25a37bf74f..e9fca6afba 100644
--- a/manifests/v2/base/rbac/kustomization.yaml
+++ b/manifests/v2/base/rbac/kustomization.yaml
@@ -2,3 +2,5 @@ resources:
   - role.yaml
   - role_binding.yaml
   - service_account.yaml
+# TODO (andreyvelich): Move it to overlays once we copy the JobSet manifests.
+namespace: kubeflow-system
diff --git a/manifests/v2/base/runtimes/pre-training/kustomization.yaml b/manifests/v2/base/runtimes/pre-training/kustomization.yaml
new file mode 100644
index 0000000000..1fb6985131
--- /dev/null
+++ b/manifests/v2/base/runtimes/pre-training/kustomization.yaml
@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - torch-distributed.yaml
diff --git a/manifests/v2/base/runtimes/pre-training/torch-distributed.yaml b/manifests/v2/base/runtimes/pre-training/torch-distributed.yaml
new file mode 100644
index 0000000000..a28523de0e
--- /dev/null
+++ b/manifests/v2/base/runtimes/pre-training/torch-distributed.yaml
@@ -0,0 +1,33 @@
+apiVersion: kubeflow.org/v2alpha1
+kind: ClusterTrainingRuntime
+metadata:
+  name: torch-distributed
+  labels:
+    training.kubeflow.org/phase: pre-training
+spec:
+  mlPolicy:
+    numNodes: 1
+    torch:
+      numProcPerNode: auto
+  template:
+    spec:
+      replicatedJobs:
+        - name: trainer-node
+          template:
+            spec:
+              template:
+                spec:
+                  containers:
+                    - name: trainer
+                      image: pytorch/pytorch:2.5.0-cuda12.4-cudnn9-runtime
+                      command:
+                        - /bin/bash
+                        - -c
+                        - |
+                          echo "Torch Distributed Runtime"
+
+                          echo "--------------------------------------"
+                          echo "Torch Default Runtime Env"
+                          env | grep PET_
+
+                          pip list
diff --git a/manifests/v2/base/webhook/kustomization.yaml b/manifests/v2/base/webhook/kustomization.yaml
index 5723808d02..1ea670ceef 100644
--- a/manifests/v2/base/webhook/kustomization.yaml
+++ b/manifests/v2/base/webhook/kustomization.yaml
@@ -10,3 +10,5 @@ patches:
       kind: ValidatingWebhookConfiguration
 configurations:
   - kustomizeconfig.yaml
+# TODO (andreyvelich): Move it to overlays once we copy the JobSet manifests.
+namespace: kubeflow-system
diff --git a/manifests/v2/overlays/only-manager/kustomization.yaml b/manifests/v2/overlays/only-manager/kustomization.yaml
new file mode 100644
index 0000000000..b6f81239d8
--- /dev/null
+++ b/manifests/v2/overlays/only-manager/kustomization.yaml
@@ -0,0 +1,18 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - namespace.yaml
+  - ../../base/crds
+  - ../../base/manager
+  - ../../base/rbac
+  - ../../base/webhook
+  # TODO (andreyvelich): JobSet should support kubeflow-system namespace.
+  - https://github.com/kubernetes-sigs/jobset/releases/download/v0.6.0/manifests.yaml
+images:
+  - name: kubeflow/training-operator-v2
+    newTag: latest
+secretGenerator:
+  - name: training-operator-v2-webhook-cert
+    namespace: kubeflow-system
+    options:
+      disableNameSuffixHash: true
diff --git a/manifests/v2/overlays/only-manager/namespace.yaml b/manifests/v2/overlays/only-manager/namespace.yaml
new file mode 100644
index 0000000000..6bfc4968bd
--- /dev/null
+++ b/manifests/v2/overlays/only-manager/namespace.yaml
@@ -0,0 +1,4 @@
+apiVersion: v1
+kind: Namespace
+metadata:
+  name: kubeflow-system
diff --git a/manifests/v2/overlays/only-runtimes/kustomization.yaml b/manifests/v2/overlays/only-runtimes/kustomization.yaml
new file mode 100644
index 0000000000..41fb29b783
--- /dev/null
+++ b/manifests/v2/overlays/only-runtimes/kustomization.yaml
@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - ../../base/runtimes/pre-training
diff --git a/manifests/v2/overlays/standalone/kustomization.yaml b/manifests/v2/overlays/standalone/kustomization.yaml
index 1ddb0a6f9e..2a59e17ed4 100644
--- a/manifests/v2/overlays/standalone/kustomization.yaml
+++ b/manifests/v2/overlays/standalone/kustomization.yaml
@@ -2,7 +2,11 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
   - namespace.yaml
-  - ../../base
+  - ../../base/crds
+  - ../../base/manager
+  - ../../base/rbac
+  - ../../base/webhook
+  - ../../base/runtimes/pre-training
   # TODO (andreyvelich): JobSet should support kubeflow-system namespace.
   - https://github.com/kubernetes-sigs/jobset/releases/download/v0.6.0/manifests.yaml
 images: