Hello Mr. Tony Montana!
There are two ways.
1) you have rebuild your pop-ups in FW and put it exactly in the place where it should be on your HTML page (for example, you want it to be in the center and 20 pixels from top - build your pop-ups in the center and 20 pixels from top).
2) fix it manually. In your HTML editor (it's DreamWeaver, isn't it?) click on the menu that calls pop-up menu, go to source code and find code that responsible for positioning of pop-up menu. It should look like this:
<a href="#" onMouseOut="MM_swapImgRestore();FW_startTimeout()" onMouseOver="window.FW_showMenu(window.fw_menu_0,59,74);MM_swapImage('site_map','','some_img_over.gif',1);" >
<img name="some_name" src="some_img.gif" width="59" height="23" border="0" align="middle">
</a>
those two numbers are responsible for positioning of your pop-up menu - first one is X coordinate and the other is Y. Change it to find the exact place where you want your pop-up menu appear.
This way seems for me better than first one 'cause it ensures you about the exact place where pop-up menu will appear.
Good Luck!