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This question comes up at times. MOSFET sources and drains are the same, so you can swap them without changing circuit behavior. At the moment, the extractor picks which side is source or drain arbitrarily.

If you insist on having source and drain in the order you intend, you can create a point label (zero size box) at the boundary between gate and source (or drain) with the text "`S$`" (or "`D$`"). That is the only label format that magic will recognize as identifying a transistor source or drain.

If you’re having trouble with netgen LVS, be sure that you specify the setup file on the command line. If you don’t, parallel devices ar not reduced source and drain may mismatch.