First, should it be plural 'tools'? If he keeps one tool in its proper place, he can keep all his tools in their proper places. If that's a well-organized systen of places, then he is thereby keeping them organized (that is, in an organized pattern of places).
He probably also keeps them in good repair: another non-literal (non-physical?) use of 'keep'. He makes sure they are always well repaired, so they keep on (continue) being in good repair.