You can just list the scripts that you want to be installed in Makefile.am:
bin_SCRIPTS = foo bar
This will cause foo and bar to be installed during make install. To get the path to their final location, you can use @bindir@ in foo.in and let configure build foo for you. For example, in configure.ac:
AC_CONFIG_FILES([foo bar])
and then in foo.in:
#!/bin/sh
prefix=@prefix@
exec_prefix=@exec_prefix@
bindir=@bindir@
echo bindir = $bindir
Keep in mind that the person running configure may specify any of --prefix, --exec_prefix, or
--bindir, and the installation may be redirected with a DESTDIR. Using the technique described here, DESTDIR will not be taken into account and the script will be installed in a location other than the path that it will echo. This is by design, and is the correct behavior, as usually a DESTDIR installation is used to create a tarball that will eventually be unpacked into the filesystem in such a way that the bindir in the script becomes valid.