As usual:
 ./configure
 make

Js2Scheme does not have any install-target (although it should be very easy
to add it).

The easiest way to compile programs is to use the js2scm-comp script. It
uses some targets in the Makefile to simplify the compilation.

You can also look at the repl-directory for a small example.

Note: js2scheme is quite complete, but far from perfect.
The biggest problem is that the generated files are huge. I haven't spent much
time on improving the situation, so maybe a solution is straight-forward.