If you want to modify the Linux kernel sources instead, insert the following commands to create an image of the actual used sources:
pengwyn@pengwyn-desktop:~$ mkdir -p /home/pengwyn/Documents/linux-kernel
pengwyn@pengwyn-desktop:~$ cd /home/pengwyn/Documents/linux-kernel
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ cp /home/pengwyn/yocto/poky/meta-silica/recipes-kernel/linux/linux-pengwyn-3.2/linux-pengwyn* .
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ tar -xzf linux-pengwyn_3.2.tar.gz
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ mv linux-pengwyn_3.2 a
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ patch -p1 -d a/ < linux-pengwyn_3.2.patch
patching file ...
...
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ cp -r a/ b/
Modify the sources contained inside directory b, than create your patch
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ diff -Naur a/ b/ > linux-pengwyn_3.2.mine.patch
pengwyn@pengwyn-desktop:~/Documents/linux-kernel$ cp linux-pengwyn_3.2.mine.patch /home/pengwyn/yocto/poky/meta-silica/recipes-kernel/linux/linux-pengwyn-3.2/
Create a file named linux-pengwyn_3.2.bbappend inside directory /home/pengwyn/yocto/poky/meta-silica/recipes-kernel/linux/ and write the following text inside the .bbappend file:
SRC_URI += "file://linux-pengwyn_3.2.mine.patch \
"
Clean and build:
bitbake linux-pengwyn -c cleanall
bitbake linux-pengwyn