diff --git a/Makefile b/Makefile
index 0c62080..fa5c150 100644
--- a/Makefile
+++ b/Makefile
@@ -119,8 +119,8 @@ test-integration: manifests fmt vet envtest ginkgo ## Run integration tests.
 	$(GINKGO) --junit-report=junit.xml --output-dir=$(ARTIFACTS) -v $(INTEGRATION_TARGET)
 
 .PHONY: test-e2e
-test-e2e: kustomize manifests fmt vet envtest ginkgo kind-image-build
-	E2E_KIND_VERSION=$(E2E_KIND_VERSION) KIND_CLUSTER_NAME=$(KIND_CLUSTER_NAME) KIND=$(KIND) KUBECTL=$(KUBECTL) KUSTOMIZE=$(KUSTOMIZE) GINKGO=$(GINKGO) USE_EXISTING_CLUSTER=$(USE_EXISTING_CLUSTER) IMAGE_TAG=$(IMG) ./hack/e2e-test.sh
+test-e2e: kustomize manifests fmt vet envtest ginkgo kind-image-build kind-agent-image-build
+	E2E_KIND_VERSION=$(E2E_KIND_VERSION) KIND_CLUSTER_NAME=$(KIND_CLUSTER_NAME) KIND=$(KIND) KUBECTL=$(KUBECTL) KUSTOMIZE=$(KUSTOMIZE) GINKGO=$(GINKGO) USE_EXISTING_CLUSTER=$(USE_EXISTING_CLUSTER) IMAGE_TAG=$(IMG) AGENT_IMAGE_TAG=$(AGENT_IMG) ./hack/e2e-test.sh
 
 GOLANGCI_LINT = $(shell pwd)/bin/golangci-lint
 GOLANGCI_LINT_VERSION ?= v1.58.2
@@ -200,6 +200,11 @@ kind-image-build: PLATFORMS=linux/amd64
 kind-image-build: IMAGE_BUILD_EXTRA_OPTS=--load
 kind-image-build: kind image-build
 
+.PHONY: kind-agent-image-build
+kind-agent-image-build: PLATFORMS=linux/amd64
+kind-agent-image-build: IMAGE_BUILD_EXTRA_OPTS=--load
+kind-agent-image-build: kind agent-image-build
+
 ##@ Deployment
 
 ifndef ignore-not-found
@@ -275,10 +280,12 @@ artifacts: kustomize
 	if [ -d artifacts ]; then rm -rf artifacts; fi
 	mkdir -p artifacts
 	$(KUSTOMIZE) build config/default -o artifacts/manifests.yaml
-	@$(call clean-manifests)
 
-	# Merge all the yamls, inclduing the agent.
-	./hack/merge-yaml.sh
+	echo "---" >> artifacts/manifests.yaml
+
+	cd agent/config/manager && $(KUSTOMIZE) edit set image controller=${AGENT_IMG}
+	$(KUSTOMIZE) build agent/config >> artifacts/manifests.yaml
+	@$(call clean-manifests)
 
 HELMIFY ?= $(LOCALBIN)/helmify
 
diff --git a/agent/deploy/clusterrole-binding.yaml b/agent/config/base/clusterrole-binding.yaml
similarity index 90%
rename from agent/deploy/clusterrole-binding.yaml
rename to agent/config/base/clusterrole-binding.yaml
index 3954691..f8d48ec 100644
--- a/agent/deploy/clusterrole-binding.yaml
+++ b/agent/config/base/clusterrole-binding.yaml
@@ -5,7 +5,7 @@ metadata:
 subjects:
 - kind: ServiceAccount
   name: manta-agent
-  namespace: manta-system
+  namespace: system
 roleRef:
   kind: ClusterRole
   name: manta-agent-role
diff --git a/agent/deploy/clusterrole.yaml b/agent/config/base/clusterrole.yaml
similarity index 100%
rename from agent/deploy/clusterrole.yaml
rename to agent/config/base/clusterrole.yaml
diff --git a/agent/deploy/serviceaccount.yaml b/agent/config/base/serviceaccount.yaml
similarity index 71%
rename from agent/deploy/serviceaccount.yaml
rename to agent/config/base/serviceaccount.yaml
index 0f4d589..ac263cf 100644
--- a/agent/deploy/serviceaccount.yaml
+++ b/agent/config/base/serviceaccount.yaml
@@ -2,4 +2,4 @@ apiVersion: v1
 kind: ServiceAccount
 metadata:
   name: manta-agent
-  namespace: manta-system
+  namespace: system
diff --git a/agent/config/kustomization.yaml b/agent/config/kustomization.yaml
new file mode 100644
index 0000000..3f2107d
--- /dev/null
+++ b/agent/config/kustomization.yaml
@@ -0,0 +1,8 @@
+# Adds namespace to all resources.
+namespace: manta-system
+
+resources:
+- ./manager
+- ./base/serviceaccount.yaml
+- ./base/clusterrole.yaml
+- ./base/clusterrole-binding.yaml
diff --git a/agent/deploy/daemonset.yaml b/agent/config/manager/daemonset.yaml
similarity index 95%
rename from agent/deploy/daemonset.yaml
rename to agent/config/manager/daemonset.yaml
index 99715f3..d1c34ec 100644
--- a/agent/deploy/daemonset.yaml
+++ b/agent/config/manager/daemonset.yaml
@@ -25,7 +25,8 @@ spec:
             mountPath: /workspace/models
       containers:
       - name: agent
-        image: inftyai/manta-agent:v0.0.2
+        image: controller:latest
+        imagePullPolicy: IfNotPresent
         ports:
         - containerPort: 9090
         resources:
diff --git a/agent/config/manager/kustomization.yaml b/agent/config/manager/kustomization.yaml
new file mode 100644
index 0000000..10f93fc
--- /dev/null
+++ b/agent/config/manager/kustomization.yaml
@@ -0,0 +1,8 @@
+resources:
+- daemonset.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+images:
+- name: controller
+  newName: inftyai/manta-agent
+  newTag: v0.0.2
diff --git a/config/manager/kustomization.yaml b/config/manager/kustomization.yaml
index c257655..931ffb9 100644
--- a/config/manager/kustomization.yaml
+++ b/config/manager/kustomization.yaml
@@ -4,5 +4,5 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 images:
 - name: controller
-  newName: inftyai/test
-  newTag: manta-111113
+  newName: inftyai/manta
+  newTag: v0.0.2
diff --git a/hack/e2e-test.sh b/hack/e2e-test.sh
index 0edb596..054654c 100755
--- a/hack/e2e-test.sh
+++ b/hack/e2e-test.sh
@@ -34,10 +34,17 @@ function startup {
 }
 function kind_load {
     $KIND load docker-image $IMAGE_TAG --name $KIND_CLUSTER_NAME
+    $KIND load docker-image $AGENT_IMAGE_TAG --name $KIND_CLUSTER_NAME
 }
 function deploy {
+    # controller
     cd $CWD/config/manager && $KUSTOMIZE edit set image controller=$IMAGE_TAG
     $KUSTOMIZE build $CWD/test/e2e/config | $KUBECTL apply --server-side -f -
+
+    # agent
+	cd $CWD/agent/config/manager && $KUSTOMIZE edit set image controller=$AGENT_IMAGE_TAG
+    $KUSTOMIZE build $CWD/agent/config | $KUBECTL apply --server-side -f -
+
 }
 trap cleanup EXIT
 startup
diff --git a/hack/merge-yaml.sh b/hack/merge-yaml.sh
deleted file mode 100755
index 4c89150..0000000
--- a/hack/merge-yaml.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-# Copyright 2024 The Kubernetes Authors.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-set -o errexit
-set -o nounset
-set -o pipefail
-
-output_file="artifacts/manifests.yaml"
-
-for file in agent/deploy/*.yaml; do
-    echo "---" >> "$output_file"
-    cat "$file" >> "$output_file"
-done
diff --git a/test/e2e/suit_test.go b/test/e2e/suit_test.go
index 1531eb0..00ff7b8 100644
--- a/test/e2e/suit_test.go
+++ b/test/e2e/suit_test.go
@@ -101,8 +101,6 @@ func readyForTesting(client client.Client) {
 	}).ShouldNot(Succeed())
 
 	By("waiting for nodeTrackers to ready")
-	// Hardcoded the namespace here because we just can't change the namespace dynamically.
-	Expect(util.Apply(ctx, k8sClient, "../../agent/deploy", "manta-system", "create")).To(Succeed())
 	Eventually(func() error {
 		nodeTrackers := &api.NodeTrackerList{}
 		if err := client.List(ctx, nodeTrackers); err != nil {