constrained QEq

What you are talking about ressembles the QEq with conserved charges within each molecule, as explained by Bauer, Patel, Theor Chem Acc (2012) 131:1153 DOI 10.1007/s00214-012-1153-7 (The way they construct the QEq matrix is slightly different from the one of Rappe and Goddard.)
In any case all of the atoms have to be in the QEq scheme, since it contains the Coulomb interaction J_{ij}. Otherwise the polarizable sites won’t feel the non-polarizable ones.