possible? Put file & containing directories from Root

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So I don't know what to say it is that I want... I can describe it...

When working on my work computer using Dreamweaver CS4 / CS5 the files that I modify and then put to server are put into the proper directory relative to /root and if the server doesn't have them (say I nested a modified.html file in a series of directories during a reorganization) the directories are added to /root

From what I know of WinSCP, when I put a file (drag / drop) I have to move the file directly into the directory in which I want it to land... if I don't then I have put modified.html files into wrong directory. While yes I could drag the parent directory each time (e.g. root/products/big-widgets/modified.html) that would mean redundancy or possible error when the directories already have existing files...

I tried reading Wiki on WinSCPbut got lost in wading through all that I already understood about program and didn't have an effective way of search for what it is I'm hoping to have happen.

Input please?

thanks
Casey
working from home....

I'm not sure I undwerstand. Are you editing files in Dreamweaver and uploading them with WinSCP? Or are you comparing how you work with Dreamwaver vs. WinSCP?