in the patch file you should see how the diff was made,

• i usually use

  diff -r -c xpilot-4.1.0_orig/src/ xpilot-4.1.0/src/ > patchfile

  or

  diff -w -r -c xpilot-4.1.0_orig/src/ xpilot-4.1.0/src/ > patchfile

  the former is a recursive (-r) context (-c) diff, which is easy to read,
  the latter additionally doesn't pay attention to differences in whitespaces (-w)

• and these diffs can be applied with
  cd xpilot-4.1.0/
  and

  patch -p1 -i patchfile
  

  for the former diff or

  patch -l -p1 -i patchfile
  

  for the latter, applying loose (-l) according to whitespaces.

• If you use the option -p1 (p for path, truncate 1 part of it) - like above - when you are in the xpilot directory,
  then it doesn't matter what the name of this directory actually is.
  You might have renamed it (as it is a special version) or the author of the diff did this...