I am not familiar with CuteFTP but I understand the issue you have with FileZilla and not being able to edit files quickly and easily via the FTP interface. I use a combination of the Cofee Cup FTP program - which used to be free - not sure if they are charging for the latest edition. Even if they are it is probably very affordable. I do rely heavily on FileZilla for bulk FTP jobs - as it had the very nice failure alerts, etc. I have yet to have any issues with large installs - which used to give me fits when I tried doing large jobs with Coffee Cup. So - I upload w FZ and tweak and edit with CC - that's my .02 on this - as I know your pain chasing one or two minor corrupted files and php errors...

Good Luck