diff --git a/scripts/launch_vllm.py b/scripts/launch_vllm.py
index e3e3e682a..7d7899308 100644
--- a/scripts/launch_vllm.py
+++ b/scripts/launch_vllm.py
@@ -2,6 +2,7 @@
 import json
 import os
 import sys
+import warnings
 
 
 def parse_args():
@@ -9,7 +10,7 @@ def parse_args():
         description="Launch vLLM for hidden states extraction",
         usage=(
             "launch_vllm.py [-h] MODEL [--hidden-states-path HIDDEN_STATES_PATH] "
-            "[--layers LAYERS [LAYERS ...]] -- *VLLM_ARGS"
+            "[--target-layer-ids TARGET_LAYER_IDS [TARGET_LAYER_IDS ...]] -- *VLLM_ARGS"
         ),
     )
     parser.add_argument(
@@ -22,12 +23,13 @@ def parse_args():
         help="The directory to save hidden states to. Default '/tmp/hidden_states'.",
     )
     parser.add_argument(
-        "--layers",
+        "--target-layer-ids",
         type=int,
         nargs="+",
         help=(
-            "(Optional) A (space separated) list of integer layer ids. Default layers "
-            "[2, num_hidden_layers // 2, num_hidden_layers - 3, num_hidden_layers]."
+            "(Optional) A (space separated) list of integer layer ids. Defaults to "
+            "[2, num_hidden_layers // 2, num_hidden_layers - 3, num_hidden_layers]. "
+            "Note: if set, you must also pass the same value into the training process"
         ),
     )
     parser.add_argument(
@@ -43,10 +45,15 @@ def main():
     if "--" in vllm_args:
         vllm_args.remove("--")
 
-    if args.layers:
-        layers = args.layers
+    if args.target_layer_ids:
+        target_layer_ids = args.target_layer_ids
+        warnings.warn(
+            f"Using custom target layer ids {args.target_layer_ids}. These "
+            "must also be explicitly passed into the training script.",
+            stacklevel=2,
+        )
     else:
-        # Import here so that it isn't required if layers passed explicitly
+        # Import here so that it isn't required if target_layer_ids passed explicitly
         from transformers import AutoConfig  # noqa: PLC0415
 
         config = AutoConfig.from_pretrained(args.model)
@@ -54,13 +61,18 @@ def main():
             config = config.text_config
 
         num_hidden_layers = config.num_hidden_layers
-        layers = [2, num_hidden_layers // 2, num_hidden_layers - 3, num_hidden_layers]
+        target_layer_ids = [
+            2,
+            num_hidden_layers // 2,
+            num_hidden_layers - 3,
+            num_hidden_layers,
+        ]
 
     speculative_config = {
         "method": "extract_hidden_states",
         "num_speculative_tokens": 1,
         "draft_model_config": {
-            "hf_config": {"eagle_aux_hidden_state_layer_ids": layers}
+            "hf_config": {"eagle_aux_hidden_state_layer_ids": target_layer_ids}
         },
     }
     kv_transfer_config = {
diff --git a/scripts/train.py b/scripts/train.py
index 1490bad40..7c7bf3189 100644
--- a/scripts/train.py
+++ b/scripts/train.py
@@ -437,7 +437,16 @@ def parse_args():
         help="Architecture for draft decoder layers. Defaults to 'llama'. "
         "Note: only 'llama' is currently supported in vLLM for inference.",
     )
-
+    parser.add_argument(
+        "--target-layer-ids",
+        type=int,
+        nargs="+",
+        help=(
+            "(Optional) A (space separated) list of integer layer ids. Defaults to"
+            "[2, num_hidden_layers // 2, num_hidden_layers - 3, num_hidden_layers]. "
+            "Note: must be set explicitly if custom values were used to launch vllm"
+        ),
+    )
     parser.add_argument(
         "--token-freq-path",
         type=str,
diff --git a/src/speculators/models/eagle3/core.py b/src/speculators/models/eagle3/core.py
index 0f07e0da1..15077e6fd 100644
--- a/src/speculators/models/eagle3/core.py
+++ b/src/speculators/models/eagle3/core.py
@@ -548,12 +548,27 @@ def from_training_args(
         Returns:
             Initialized Eagle3DraftModel
         """
+        target_layer_ids = kwargs.get("target_layer_ids")
+        if target_layer_ids is None:
+            unmodified_verifier_config = AutoConfig.from_pretrained(
+                kwargs["verifier_name_or_path"]
+            )
+            num_target_layers = unmodified_verifier_config.num_hidden_layers
+            target_layer_ids = [2, num_target_layers // 2, num_target_layers - 3]
+            warnings.warn(
+                "--target-layer-ids is not explicitly set. Setting target "
+                f"layers to {target_layer_ids}. If custom target layers were used "
+                "when launching vllm datagen, please set them explicitly.",
+                stacklevel=2,
+            )
+
         config = Eagle3SpeculatorConfig(
             transformer_layer_config=verifier_config,
             draft_vocab_size=kwargs["draft_vocab_size"],
             norm_before_residual=kwargs["norm_before_residual"],
             norm_before_fc=kwargs.get("norm_before_fc", False),
             embed_requires_grad=kwargs.get("embed_requires_grad", False),
+            eagle_aux_hidden_state_layer_ids=target_layer_ids,
             speculators_config=SpeculatorsConfig(
                 algorithm="eagle3",
                 proposal_methods=[
diff --git a/tests/unit/train/test_setup_model.py b/tests/unit/train/test_setup_model.py
index d82f2ae9e..eeb3982d0 100644
--- a/tests/unit/train/test_setup_model.py
+++ b/tests/unit/train/test_setup_model.py
@@ -761,7 +761,7 @@ def test_from_training_args_loads_vocab_mappings(vocab_mappings):
             draft_vocab_size=DRAFT_VOCAB_SIZE,
             norm_before_residual=False,
             ttt_steps=1,
-            verifier_name_or_path="dummy",
+            verifier_name_or_path="nm-testing/tinysmokellama-3.2",
         )
 
     assert model.t2d is not None, "t2d is None after from_training_args"