Yes Kelly, you can do exactly that.
With you ftp program opened, click on temp file folder, hold down your mouse and drag it to the position you want it to be. With that done, you can rename the folder if you choose.
Now if you want to move the contents of the temp folder to the root of this directory, you can do one of two things, you could download your entire folder and it contents then upload everything inside the folder but not the folder to your root directory. Or you could simply click on the items you want to move while holding down the shift key and drag them to the position you want them to be. Much more simple once you've tried it a few times.
One problem you may run into is running out of window space in you ftp, but don't worry, this is how you handle it. Your ftp program should have 4 windows - 2 for your computer files and two displaying your server files. On your server side, find your folder, click to open the content in the bottom window - the bottom window is now ready, now adjust the top window until you can see the directory where you want to put it, ok now follow the instructions above and drag everything and drop, yes even crossing the divider between the two sections. Is done. Very easy really.