In my capacitors, there's an extra node called VSUBS, even though I do not have that node labeled. Is that connected to a pin on the harness or I need to do it manually? Would it be from the pwell?

VSUBS is the default substrate node. If there are no connections to devices in a subcircuit, it usually passes LVS at a higher level. These are mim capacitors, right?

Yes, that's correct

If LVS passes, I'd say no worries.

Do you mean like using netgen?

Yes.

sounds good. thanks!