I'f I were doing it, First, I would keep the -12V separated from anything on the AC side (N or Ground).
Second, I would route a VSS (5V regulator common, bypass caps, anything that touches the uP) trace up to the edge of the board where the connector from the 12V supply comes in, but would connect it to its own pin on the connector, an place it next-to, but not connected to -12V.
Third, I would route a -12V trace where ever it needs to go on the board. Any bypass cap from +12V returns on -12V (not on Vss). Any bypass cap on the output of the 5V regulator returns to Vss (not to -12V)
To make the system work, eventually Vss must tied to -12V. You have two choices. 1. Install a jumper at the connector because Vss is next to -12V. 2. Carry separate wires back to the 12V supply, and common Vss to -12V there. Which you do in production depends on which one works better...
Do not intermix Vss and -12V traces on the board...