The patch in summary is touching both Makefile.in and Makefile.am, probably to avoid autotools rebuild.
This treatment is usually reserved for a few selected system packages that cannot have their autotool scripts rebuilt.
This _could_ cause maintainermode-driven rebuild (see http://blog.flameeyes.eu/articles/2008/06/13/maintaner-mode ), which is something we should be avoiding as much as possible.
Please just patch Makefile.am and/or configure.in/.ac and rebuild autotools, unless you have very good reasons not to.
Patching order is correct (.am before .in) and does not cause maintainer-mode reconfigure.