Sorry i misunderstood. The way you said it seemed odd.
You can absolutely do what you want to do. Say you had 3 nodes (A,B,C) and 2 clustered SQL instances.(S1,S2).
You would just choose where to install the binaries for S1 & S2.
So for example A & B would have the binaries for S1 installed.
B & C would have the binaries for S2 installed.
That way each SQL instance would have 2 possible homes.
But on a side note why not just go ahead and install the binaries for S1 & S2 on A,B & C that way, just in case , you have another failover location. You could during normal times not allow the 3rd node to be an owner of the SQL instance but in an emergency you could just check a box and fail it there (strange patching error or something...).