you should 'reify' your conditions, posting constraints of the form
reify(A,B,C) :- C #<==> A #= B.
between pairs of variables. maplist/3 it's an handy shortcut
:- use_module(library(clpfd)).
% simulate domain/3 in SWI-prolog
domain(Vs,L,H) :- Vs ins L..H.
reify(A,B,C) :-
C #<==> A #= B.
main(A,B,C) :-
length(A,3),
domain(A,1,3),
all_different(A),
length(B,3),
domain(B,1,3),
all_different(B),
maplist(reify, A,B,C),
labeling([],A),
labeling([],B).
yields
1 ?- main(A,B,C).
A = B, B = [1, 2, 3],
C = [1, 1, 1] ;
A = [1, 2, 3],
B = [1, 3, 2],
C = [1, 0, 0] ;
A = [1, 2, 3],
B = [2, 1, 3],
C = [0, 0, 1]
etc ....