Just cut and paste from one place to the other.
Select the first song then hold the shift key down and select the last song in that directory (this will select all the songs in that directory) then just use the menu to cut them from there - open the other directory and go to the menu and just select paste.
This should then transfer all the files from one directory into the other depending on which one you want to keep. You can even drag them into the new directory if you're using the navigation view that has all your folder appearing on one side of the window and the open directory showing on the other side of the dividing line.
You can get this appearance by going into your "Windows Explorer" view or by selecting "Computer" on the desktop and then selecting "organise" followed by Layout and then setting it so that the "navigation" view is the one you use to view your files. It also makes it a lot easier to get around in Windows Explorer if you have this "navigation" pane showing. It saves a lot of going upward and downward in your computer view. Everything is layed out in front of you and you can move files around in a much easier manner.
It's sometimes better to have them in two different directories anyhow. That way you get to choose what and how many files you want to share. In my case I have 3 folders... one called "Downloaded Music" which is under my name directory "Robert" (accessed from the desktop) that's where all the newly downloaded songs go. And the next one is called "Shared Music" under my main directory C:\ (accessed from "Computer" on the desktop) which has about 300 files in it and I keep the other 2000 odd songs in a folder called "My Music". (also under "Computer") That way I can decide how many files I wish to share (300) instead of having all my files shared by having the C:\My Music selected as the folder i want to share with the Limewire community.
Unfortunately sometimes having all your songs available to share means you are constantly having other people downloading songs from your computer and this slows your downloading down a bit. By only sharing the 300 I have decided which files I want to share and that way people are not constantly downloading from my selection of songs.