I understand that the program called "ftp" is intended for interactive use by a human. I don't think that it's a good idea to try to abuse it for automation.
Unless you find an appropriate uploading command line utility (such as wget for downloading), I suppose you need to write the protocol handling in C (maybe there is a decent ftrp library somewhere, that you can use).
ncftp is a package for PCs that containf ncftpput which seems to do what you want.
Here
http://linux.wareseeker.com/free-thin-ftp-upload/ (
http://linux.wareseeker.com/free-thin-ftp-upload/) there seem to be several more examples.
You might try to port some of this to NIOS uClinux or extract some code to include in your application.
-Michael