diff --git a/Containerfile b/Containerfile
index 03c5b6f..56ded2b 100644
--- a/Containerfile
+++ b/Containerfile
@@ -5,7 +5,12 @@ FROM ${BASE_CONTAINER_URL}:${FEDORA_MAJOR_VERSION}
 ARG RECIPE
 
 # copy over configuration files
-COPY etc /etc
+# etc is copied to /usr/etc/ to prevent "merge conflicts"
+# as it is the proper directory for "system" configuration files
+# and /etc/ is for editing by the local admin
+# see issue #28 (https://github.com/ublue-os/startingpoint/issues/28)
+COPY etc /usr/etc
+# uncomment below line if you need to put config files in /usr/
 # COPY usr /usr
 
 # copy scripts
diff --git a/build.sh b/build.sh
index df60f8c..d1354f3 100644
--- a/build.sh
+++ b/build.sh
@@ -23,9 +23,9 @@ echo "---"
 pip install --prefix=/usr yafti
 
 # add a package group for yafti using the packages defined in recipe.yml
-yq -i '.screens.applications.values.groups.Custom.description = "Flatpaks defined by the image maintainer"' /etc/yafti.yml
-yq -i '.screens.applications.values.groups.Custom.default = true' /etc/yafti.yml
+yq -i '.screens.applications.values.groups.Custom.description = "Flatpaks defined by the image maintainer"' /usr/etc/yafti.yml
+yq -i '.screens.applications.values.groups.Custom.default = true' /usr/etc/yafti.yml
 flatpaks=$(yq '.flatpaks[]' < /tmp/ublue-recipe.yml)
 for pkg in $(echo -e "$flatpaks"); do \
-    yq -i ".screens.applications.values.groups.Custom.packages += [{\"$pkg\": \"$pkg\"}]" /etc/yafti.yml
+    yq -i ".screens.applications.values.groups.Custom.packages += [{\"$pkg\": \"$pkg\"}]" /usr/etc/yafti.yml
 done
diff --git a/etc/justfile b/etc/justfile
index 18fab55..5e655aa 100644
--- a/etc/justfile
+++ b/etc/justfile
@@ -26,7 +26,7 @@ distrobox-ubuntu:
 setup-flatpaks:
   #!/bin/bash
   echo 'Installing flatpaks from the ublue recipe ...'
-  flatpaks=$(yq '.flatpaks[]' < /etc/ublue-recipe.yml)
+  flatpaks=$(yq '.flatpaks[]' < /usr/etc/ublue-recipe.yml)
   for pkg in $flatpaks; do \
       echo "Installing: ${pkg}" && \
       flatpak install --user --noninteractive flathub $pkg; \
diff --git a/etc/profile.d/ublue-firstboot.sh b/etc/profile.d/ublue-firstboot.sh
index 62818cd..fe1d6b6 100644
--- a/etc/profile.d/ublue-firstboot.sh
+++ b/etc/profile.d/ublue-firstboot.sh
@@ -1,6 +1,6 @@
 if test "$(id -u)" -gt "0" && test -d "$HOME"; then
     if test ! -e "$HOME"/.config/autostart/ublue-firstboot.desktop; then
         mkdir -p "$HOME"/.config/autostart
-        cp -f /etc/skel.d/.config/autostart/ublue-firstboot.desktop "$HOME"/.config/autostart
+        cp -f /usr/etc/skel.d/.config/autostart/ublue-firstboot.desktop "$HOME"/.config/autostart
     fi
 fi
\ No newline at end of file
diff --git a/etc/skel.d/.config/autostart/ublue-firstboot.desktop b/etc/skel.d/.config/autostart/ublue-firstboot.desktop
index 94e94d2..bd6da13 100644
--- a/etc/skel.d/.config/autostart/ublue-firstboot.desktop
+++ b/etc/skel.d/.config/autostart/ublue-firstboot.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Name=uBlue First Boot Setup
 Comment=Sets up uBlue Desktop Correctly On FirstBoot
-Exec=/usr/bin/yafti /etc/yafti.yml
+Exec=/usr/bin/yafti /usr/etc/yafti.yml
 Icon=org.gnome.Terminal
 Type=Application
 Categories=Utility;System;