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The crucial thing is to make Vin and Vip lines symmetric, including resistor,switches and caps. Vcm has to be as closest as possible as well. I suggest you to use unit size for all resistors and scale them with m parameters. Same for caps and switches as well. Inside the OPAMP, the most crucial...
You need to add pins/ports at the level you are running LVS. Calibre doesn't care if you have them level below because they are not related with the level you are running. You need to add pins each level if you have them in schematic.
Is your AVSS the substrate's voltage ? If that's the case, create a guard ring around your diff pair including the dummies. It's quite rare where you use the mosfet's default guardrings due to area constraints. Because if you open the guard ring options, it will bring bulk connection on each...
As a layout engineer, it depends on the resistor you use. If it has 3 pin outs in schematic, and if you have enough area in your layout, place them under n-well due to noise immunity. It will reduce the noise that resistor creates to get into substrate. You can connect to that n-well any...
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