Nesting IF in Windows Bat file

I'm not actually sure you need ELSE, let alone a nested IF, for your use case:

@echo off

IF NOT "%1%"=="0" (
    goto proc3
)
IF "%2%"=="0" ( 
    goto proc1
) 

goto proc2 

:proc1
echo in Proc1 0 0
pause
exit
:proc2
echo in Proc2 0 N0
pause
exit
:proc3
echo in Proc3 N0  0
pause
exit

If for some reason you really do want to nest your IFs, you're missing a bracket:

Your batch:

IF %1% == 0 (
    IF %2% == 0 ( goto proc1
    ) ELSE ( goto proc2
)
***MISSING )***  ELSE ( goto proc3
)

Batch that should work:

IF "%1%" == "0" (
    IF "%2%" == "0" ( 
    goto proc1
    ) ELSE ( 
    goto proc2
    )
) ELSE ( 
    goto proc3
)