“if not exist” command in batch file

if not exist "%USERPROFILE%\.qgis-custom\" (
    mkdir "%USERPROFILE%\.qgis-custom" 2>nul
    if not errorlevel 1 (
        xcopy "%OSGEO4W_ROOT%\qgisconfig" "%USERPROFILE%\.qgis-custom" /s /v /e
    )
)

You have it almost done. The logic is correct, just some little changes.

This code checks for the existence of the folder (see the ending backslash, just to differentiate a folder from a file with the same name).

If it does not exist then it is created and creation status is checked. If a file with the same name exists or you have no rights to create the folder, it will fail.

If everyting is ok, files are copied.

All paths are quoted to avoid problems with spaces.

It can be simplified (just less code, it does not mean it is better). Another option is to always try to create the folder. If there are no errors, then copy the files

mkdir "%USERPROFILE%\.qgis-custom" 2>nul 
if not errorlevel 1 (
    xcopy "%OSGEO4W_ROOT%\qgisconfig" "%USERPROFILE%\.qgis-custom" /s /v /e
)

In both code samples, files are not copied if the folder is not being created during the script execution.

EDITED – As dbenham comments, the same code can be written as a single line

md "%USERPROFILE%\.qgis-custom" 2>nul && xcopy "%OSGEO4W_ROOT%\qgisconfig" "%USERPROFILE%\.qgis-custom" /s /v /e

The code after the && will only be executed if the previous command does not set errorlevel. If mkdir fails, xcopy is not executed.