Sure does..
The patches add extra features that you need to enable with make config.
Be sure to edit Makefile to give the kernel an EXTRAVERSION different from the current kernel. This way you can still use the old kernel if the new one isn't quite right. This means installing the new kernel as a second one, modifying your boot loader etc.. Be sure the new kernel is patched the same way as the standard kernel, initrd & config, before you add patch-o-matic! (Each distro has different specific patches to their kernel)
When you build iptables, make sure it's installed in a different place from the original so you can also use the old version if it's not working ok.
Your init.d/iptables script will need to be modified to select the correct iptables depending on which kernel is running.
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