[Android Software/Hacking General [Developers Only]] v_superuser:
Okay, I'll tell this with an example.

Have a look at this vendor tree. This for Galaxy Nexus(Maguro).

Now, the important makefile, vendor-blobs.mk

In this case, it is:

# Copyright (C) 2010 The Android Open Source Project
#
# 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.

# This file is generated by device/samsung/maguro/extract-files.sh - DO NOT EDIT

# Prebuilt libraries that are needed to build open-source libraries
PRODUCT_COPY_FILES := \
vendor/samsung/maguro/proprietary/libsecril-client.so:obj/lib/libsecril-client.so

# All the blobs necessary for maguro
PRODUCT_COPY_FILES += \
vendor/samsung/maguro/proprietary/fRom:system/bin/fRom \
vendor/samsung/maguro/proprietary/libsecril-client.so:system/lib/libsecril-client.so \
vendor/samsung/maguro/proprietary/pvrsrvinit:system/vendor/bin/pvrsrvinit \
vendor/samsung/maguro/proprietary/sirfgps.conf:system/vendor/etc/sirfgps.conf \
vendor/samsung/maguro/proprietary/bcm4330.hcd:system/vendor/firmware/bcm4330.hcd \
vendor/samsung/maguro/proprietary/ducati-m3.bin:system/vendor/firmware/ducati-m3.bin \
vendor/samsung/maguro/proprietary/libpn544_fw.so:system/vendor/firmware/libpn544_fw.so \
vendor/samsung/maguro/proprietary/libEGL_POWERVR_SGX540_120.so:system/vendor/lib/egl/libEGL_POWERVR_SGX540_120.so \
vendor/samsung/maguro/proprietary/libGLESv1_CM_POWERVR_SGX540_120.so:system/vendor/lib/egl/libGLESv1_CM_POWERVR_SGX540_120.so \
vendor/samsung/maguro/proprietary/libGLESv2_POWERVR_SGX540_120.so:system/vendor/lib/egl/libGLESv2_POWERVR_SGX540_120.so \
vendor/samsung/maguro/proprietary/gps.omap4.so:system/vendor/lib/hw/gps.omap4.so \
vendor/samsung/maguro/proprietary/gralloc.omap4.so:system/vendor/lib/hw/gralloc.omap4.so \
vendor/samsung/maguro/proprietary/libglslcompiler.so:system/vendor/lib/libglslcompiler.so \
vendor/samsung/maguro/proprietary/libIMGegl.so:system/vendor/lib/libIMGegl.so \
vendor/samsung/maguro/proprietary/libinvensense_mpl.so:system/vendor/lib/libinvensense_mpl.so \
vendor/samsung/maguro/proprietary/libpvr2d.so:system/vendor/lib/libpvr2d.so \
vendor/samsung/maguro/proprietary/libpvrANDROID_WSEGL.so:system/vendor/lib/libpvrANDROID_WSEGL.so \
vendor/samsung/maguro/proprietary/libPVRScopeServices.so:system/vendor/lib/libPVRScopeServices.so \
vendor/samsung/maguro/proprietary/libsec-ril.so:system/vendor/lib/libsec-ril.so \
vendor/samsung/maguro/proprietary/libsrv_init.so:system/vendor/lib/libsrv_init.so \
vendor/samsung/maguro/proprietary/libsrv_um.so:system/vendor/lib/libsrv_um.so \
vendor/samsung/maguro/proprietary/libusc.so:system/vendor/lib/libusc.so

So, in the source code, the vendor tree is kept in /source/vendor/manufacturer/codename(vendor/samsung/maguro in this case) and the makefile parameters tell it to copy the proprietary files(that are the files in the vendor tree, for instance, open up the vendor tree's link I gave above) to certain direstories in the ROM's zip, in this case, for example, this line:

vendor/samsung/maguro/proprietary/gps.omap4.so:system/vendor/lib/hw/gps.omap4.so \

this tells the builder to copy the proprietary file gps.omap4.so to lib/hw folder in the system.

I hope you'll figure out the remaining and this cleared your doubts. ;)

PS- If I went wrong at some place, correct me. :)