Please help with beginners problem

Hi everyone.
Please forgive me if I am posting in the wrong section, but this question has elements that are related to CSS, Javascript and html, so wasn't sure where I should place my question.

I am a beginner to webdesign and learning as I go, so please forgive me if my problem is something that you'd all regard as very simple.

I have been experimenting with software called CoffeeCup DHTML editor in order to create a dynamic menu for my website which is currently under construction. I created a simple experimental dhtml menu using this program which, upon completion, automatically generates the necessary javascript code for insertion. The instructions that come with this software simply instruct to insert the automatically generated javascript into my sites html code after the body tag, and where I want the menu to be displayed. There is only this one block of code generated, and nothing else is generated to be added into the head section of my html, which is something that I have often found to be the case with other javascripts that I've used.
I have inserted this Javascript into my site code, after the body tag and 'bingo' the menu appears on my page, but it's in completely the wrong place. It displays right in the centre of my webpage and at the very top, instead of where I'd like it to be, about a third of the way down on the left-hand side. I have to say that even before inserting the javascript I guess I knew that the menu wouldn't just pop-up automatically where I needed it to be without me positioning it somehow.
So here is my problem. How do I move the menu to the exact position required? I realise that i could probably use a table to achieve this, but as someone pretty new to html I am not really sure how to insert a javascript into a table. besides, my site is based on CSS and I everything I have read tells me that I should position using CSS. But how do I position a javascript effect? I am O.K positioning images using CSS, but am really unsure how to go about this. In very simple terms (with details) what should I add to my html and/or style sheet, and where, in order to position my menu correctly?
On a final note, I gather that most menu creation software is based upon Javascript, but that it is better to achive this using pure CSS. I looked for software to create a menu using css and could only find one site - something like Open Cube? the software was quite costly, so decided to have a rethink! Are there definate benefits one way or the other - using Javascipt as opposed to CSS, and can you recommend the best software to use?
Any feedback very gratefully received.