I only started doing this two weeks ago, so I'm no expert.
First, edit the Makefile and change whatever you want.
Save it as Makefile.patched or Makefile.new (whatever).
diff -c Makefile Makefile.patched > Makefile.patch
This will produce a patch file that says what is different between the original and the patched version.
The -c option is there to give the context: the lines above and below what is changed, for easy reading.
Then delete the new version of the file and put the Makefile.patch together with the SlackBuild and the source tarball.
In the Slackbuild the patch command above will copy the patch to the current directory (should be the extracted sources), apply the patch, and change the original Makefile before compiling (I put it just before the configure & make section of the SlackBuild). The -c option is to say that this is a "context" patch, the -b is to make a backup of the original, and "-z .old" is to name the original "Makefile.old".
I prefer it this way than applying the changes in the SlackBuild, so that changes to the source code are easily documented inside the /src directory without one having to go inside the SlackBuild to find out if there are any changes at all.
If anyone cares to correct me on this stuff, I'll be glad... it works, but there might be better ways.