diff --git a/Makefile b/Makefile
index 8bfc6fd..942a69e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,3 +1,20 @@
-.PHONY: apply
-apply:
-	stow --target=$${HOME} */
+QUBES_DIRS = qubes dom0
+ALL_DIRS = $(shell ls -d */ | sed 's#/##')
+GENERAL_DIRS = $(filter-out $(QUBES_DIRS), $(ALL_DIRS))
+
+.PHONY: all apply apply-general apply-qubes clean
+
+all: apply-general apply-qubes
+
+apply-general:
+	@echo "Applying general configurations..."
+	stow --target=$(HOME) $(GENERAL_DIRS)
+
+apply-qubes:
+	@echo "Applying Qubes configurations..."
+	stow --target=/ qubes
+
+clean:
+	@echo "Removing stowed configurations..."
+	stow -D --target=$(HOME) $(GENERAL_DIRS)
+	stow -D --target=/ qubes
diff --git a/qubes/.config/qubes/dom0/etc/qubes-rpc/policy/qubes.Gpg b/dom0/etc/qubes-rpc/policy/qubes.Gpg
similarity index 100%
rename from qubes/.config/qubes/dom0/etc/qubes-rpc/policy/qubes.Gpg
rename to dom0/etc/qubes-rpc/policy/qubes.Gpg
diff --git a/qubes/.config/qubes/dom0/etc/qubes-rpc/policy/qubes.SshAgent b/dom0/etc/qubes-rpc/policy/qubes.SshAgent
similarity index 100%
rename from qubes/.config/qubes/dom0/etc/qubes-rpc/policy/qubes.SshAgent
rename to dom0/etc/qubes-rpc/policy/qubes.SshAgent
diff --git a/qubes/.config/systemd/user/qubes-ssh-socket.service b/qubes/etc/systemd/user/qubes-ssh-socket.service
similarity index 100%
rename from qubes/.config/systemd/user/qubes-ssh-socket.service
rename to qubes/etc/systemd/user/qubes-ssh-socket.service
diff --git a/qubes/.local/bin/qubes-ssh-socket b/qubes/home/user/.local/bin/qubes-ssh-socket
similarity index 100%
rename from qubes/.local/bin/qubes-ssh-socket
rename to qubes/home/user/.local/bin/qubes-ssh-socket
diff --git a/qubes/.config/qubes/appvm/rw/config/gpg-split-domain b/qubes/rw/config/gpg-split-domain
similarity index 100%
rename from qubes/.config/qubes/appvm/rw/config/gpg-split-domain
rename to qubes/rw/config/gpg-split-domain
diff --git a/qubes/.config/qubes/appvm/rw/config/qubes-bind-dirs.d/50_user.conf b/qubes/rw/config/qubes-bind-dirs.d/50_user.conf
similarity index 100%
rename from qubes/.config/qubes/appvm/rw/config/qubes-bind-dirs.d/50_user.conf
rename to qubes/rw/config/qubes-bind-dirs.d/50_user.conf