How to use if - else structure in a batch file?

I think in the question and in some of the answers there is a bit of confusion about the meaning of this pseudocode in DOS: IF A IF B X ELSE Y. It does not mean IF（A and B) THEN X ELSE Y, but in fact means IF A( IF B THEN X ELSE Y). If the test of A fails, then he whole of the inner if-else will be ignored.

As one of the answers mentioned, in this case only one of the tests can succeed so the 'else' is not needed, but of course that only works in this example, it isn't a general solution for doing if-else.

There are lots of ways around this. Here is a few ideas, all are quite ugly but hey, this is (or at least was) DOS!

@echo off

set one=1
set two=2

REM Example 1

IF %one%_%two%==1_1 (
   echo Example 1 fails
) ELSE IF %one%_%two%==1_2 (
   echo Example 1 works correctly
) ELSE (
    echo Example 1 fails
)

REM Example 2

set test1result=0
set test2result=0

if %one%==1 if %two%==1 set test1result=1
if %one%==1 if %two%==2 set test2result=1

IF %test1result%==1 (
   echo Example 2 fails
) ELSE IF %test2result%==1 (
   echo Example 2 works correctly
) ELSE (
    echo Example 2 fails
)

REM Example 3

if %one%==1 if %two%==1 (
   echo Example 3 fails
   goto :endoftests
)
if %one%==1 if %two%==2 (
   echo Example 3 works correctly
   goto :endoftests
)
echo Example 3 fails
)
:endoftests

Your syntax is incorrect. You can't use ELSE IF. It appears that you don't really need it anyway. Simply use multiple IF statements:

IF %F%==1 IF %C%==1 (
    ::copying the file c to d
    copy "%sourceFile%" "%destinationFile%"
    )

IF %F%==1 IF %C%==0 (
    ::moving the file c to d
    move "%sourceFile%" "%destinationFile%"
    )

IF %F%==0 IF %C%==1 (
    ::copying a directory c from d, /s:  boş olanlar hariç, /e:boş olanlar dahil
    xcopy "%sourceCopyDirectory%" "%destinationCopyDirectory%" /s/e
    )

IF %F%==0 IF %C%==0 (
    ::moving a directory
    xcopy /E "%sourceMoveDirectory%" "%destinationMoveDirectory%"
    rd /s /q "%sourceMoveDirectory%"
    )

Great batch file reference: http://ss64.com/nt/if.html

AFAIK you can't do an if else in batch like you can in other languages, it has to be nested if's.

Using nested if's your batch would look like

IF %F%==1 IF %C%==1(
    ::copying the file c to d
    copy "%sourceFile%" "%destinationFile%"
    ) ELSE (
        IF %F%==1 IF %C%==0(
        ::moving the file c to d
        move "%sourceFile%" "%destinationFile%"
        ) ELSE (
            IF %F%==0 IF %C%==1(
            ::copying a directory c from d, /s:  boş olanlar hariç, /e:boş olanlar dahil
            xcopy "%sourceCopyDirectory%" "%destinationCopyDirectory%" /s/e
            ) ELSE (
                IF %F%==0 IF %C%==0(
                ::moving a directory
                xcopy /E "%sourceMoveDirectory%" "%destinationMoveDirectory%"
                rd /s /q "%sourceMoveDirectory%"
                )
            )
        )
    )

or as James suggested, chain your if's, however I think the proper syntax is

IF %F%==1 IF %C%==1(
    ::copying the file c to d
    copy "%sourceFile%" "%destinationFile%"
    )