Should  I unplug my quadzilla before getting the ecm flashed for the factory high idle? 02 truck so it might not need to be flashed just the options selected.  

no need.  but if it makes you feel better go for it

Awesome thank you!

Yup. The Quad can remain hooked up during a Smarty or TSB flash for high idle. Being the Quadzilla has ZERO connection to the CCD network or the SCI network which does the actual flashing. 

What about for smog checks, does obd2 know it’s there?

No. There is no sign of the Quadzilla during smog checks (electronically) but if the inspector does a physical look then he'll see the Quadzilla some I've heard in Cally have modified the wiring and hid the Quadzilla in the cab.