Applying Linux Kernel Patches

First, clean both trees as necessary. Maybe something like a make mrproper is what you want. Create the patch one up from both trees. When you apply the patch with the following example, do it at the root of the tree you want to patch.

Create the patch:

diff -Naur old/modules/ new/modules/

Apply the patch:

patch -p1 <../patch.diff

or

bzip2 -dc ../patch.diff.bz2 | patch -p1

A set of utilities and a simply great way to manage kernel patches can be found here.