Probably you could add subroutine to CUSTOM.exe and call it from main.exe
before actually call CUSTOM.exe
Something like:
*MAIN.exe
...
set proc to CUSTON.EXE addi
llcontinue=iCheck_Custom("ETC") &&call subrotuine in CUSTOM.EXE
if llcontinue
do custom.exe && as regular
endif

>By the way: I can pass a string using this command: DO CUSTOM.EXE WITH "ETC"... But how can I get the return?