X Windows servers read X-Resources from ~/.Xdefaults or from any file in
$XAPPLRESDIR folder.

Obviously, I'd choose the second option ;-)

So, add this line to your ~/.xinitrc (possibly ~/.Xsession or ~/.Xclients, take
your pick):

  export XAPPLRESDIR=$HOME/.xresources


HINT: use "xrdb" tool for merging X-Resources without restarting your X
session. E.g.:

  xrdb -merge ~/.xresources/XTerm