Usually people put PMOS on top and NMOS on bottom, but in makes no difference. You do your layout how you feel it should be made.
Yes Nwell and Ntub are the same thing.
I did not mean that you should change the transistors. I meant that you should change the substrate contacts.
In Virtuoso, I think the default shortcut for placing contacts is "o". Place "PD_C" close to the NMOS and "ND_C" close to the PMOS (The "ND_C" should be inside the NTUB of the PMOS in order to supply the voltage to the PMOS body)
You can find out what simulator you are using in Analog Design Environement -> Setup -> Simulator/Directory/Host ...
Just a question, it looks like you draw your transistors manually or?