Well if you install it in a subdirectory it would work well with the current homepage, but of course would look different..
So, e.g.
yourdoman.com <== Your homepage with
WP and existing theme
yourdomain.com/jobs <== Your second
WP install with JobRoller
Use the built in
WP custom menus option to link the 2 sites and that's as easy as it gets ;)