I think you might be mixing up local inputs with the SQ’s 48 processing channels, which are mapped 1:1 by default but can be patched from local ports, USB, or expansion boxes like your DX168.
When you’re creating stereo pairs, you’re combining processing channels, not physical sockets. It doesn’t matter where the sockets are, just whether you’ve mapped them to an odd/even pair of processing channels.
So, in the I/O screen, you might patch sockets 7 and 8 on your DX (via the S-Link tab) to processing channels 3 and 4 (or whatever). Then, when you use the Input Stereo screen to set channels 3 and 4 as stereo, you’ll be all set.