qaac supports the following DSP options.
Note that --rate depends on libsoxr, and --lowpass, --matrix-preset, --matrix-file depend on libsoxconvolver.
Channels are internally/automatically reordered. At first, channels are reordered to the Microsoft order (such as L C R to L R C). Before encoding to AAC/ALAC, it is reordered again to AAC order (such as C L R). Of course, this reordering works properly only when the input channel layout is known. If not known, qaac uses the default guess, and it's always Microsoft order. You can use --chanmap and --chanmask to let qaac know the channel layout.
DSP chain is processed in the following order. As you can see, when matrix mixer and --chanmap is processed, channels are in Microsoft WAV order. You have to take it into account when you use these options.