(Noob). Does MS3 use CEL?
 

Once I get MS, will my Check Engine Light still perform its usual duties?

no

Some basic functionality can be implemented (eg: coming on when the engine is not running, as is expected during a smog test), but in general, no, it does not serve as a malfunction indicator. You can get a lot more information out of the ECU by plugging in your laptop rather than staring at a one-bit display.

Well, it will tell you when you've got sync errors!

--Ian

It can also do sensor's check. I've never messed with it, but it's in TunerStudio if you look in the CanBus/TestModes menu

On my MS2 I used it as a shift light. Haven't bothered trying to do the same on the MS3.

MS3 does not have full on OBD2 functionality, but it can provide some basic sensor checks. See this link for details.

Megasquirt3_TunerStudio_MS_Lite_Reference-1.4 page 277