From the same manual it follows the main purpose is that you should store all files as their are originally, not broken or binary-converted. I don't know how CuteFTP works but many times I've met problems with it. However if it works for you, that's ok.
What if every minute I would come to you and ask "what the time is"? Would it be polite? Or after 4th or 5th attempt you would lose your patience and say "hey dude, why would you simply use watch?.."
New users are more than welcome; however it doesn't mean we should repeat for everybody what's already described. Providing such questions you are simply not respecting the miniBB developers and yourself, please keep in mind we have thousands of newbie users around and answering each of you finally would stop the project at all.