What is proper process for source installs?

[Peter Steele]

We had been building systems from the binary release plus our custom kernel. In doing that we just used the base collection from the 8.0 binary release DVD and copied our kernel files to /boot/kernel. We are now doing both installworld and installkernel. The issue I'm having is figuring out what else is needed to complete the package. For example, /etc is not part of installworld, as well as a number of other text files. My inclination is to install the base package from the 8.0 binary release, and then update that set with whatever is produced by installworld. However, when I try to combine the trees I get these errors:

bin/rcp: Can't unlink already-existing object: Operation not permitted
lib/libc.so.7: Can't unlink already-existing object: Operation not permitted
lib/libcrypt.so.5: Can't unlink already-existing object: Operation not permitted
lib/libthr.so.3: Can't unlink already-existing object: Operation not permitted
libexec/ld-elf.so.1: Can't unlink already-existing object: Operation not permitted

and so on. So it's safe to say just merging the trees like this isn't the way to go. What is the proper process to finish a bsd image after installworld and installkernel is done?