You will need to generate the ftp script file from your batch.
Something like (just a skeleton)
....
set "ftpScript=%temp%\%~nx0.ftp.tmp"
(
echo open (ftp server name)
echo (ftp user-name)
echo (ftp password)
echo prompt
echo bin
echo mput "c:\user\%username%\importantfiles\*.*"
echo quit
) > "%ftpScript%"
ftp -s:"%ftpScript%"
del /q "%ftpScript%" >nul 2>nul
....