The entire menu formatting in Atahualpa is based on the
---------- DROP DOWN / FLY OUT MENUS --------------------------------
Ruthsarian's rMenu
http://webhost.bridgew.edu/etribou/layouts/
modified by Bytes For All
http://wordpress.bytesforall.com/
There are more that 400 lines of CSS that deal with the menu's. This is the singe most complicated section of CSS in the style sheet.
when you override the existing settings, you have to either, accept how it comes out or do a lot of overriding. For Example, when you change a parents CSS, it flows to the children. If you want it different then you have to add CSS to have different settings that the parent. there is the flyout, hover, current page item, parent item, and all down at multi levels.
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Here is how I figure out issues with menu's (and lots of other issues.
1) go visit your site
2) view the source code
3) copy the source code and save it to a text file and give it an extension of 'html' like 'mypage.html'
4) open the file in a browser
Now you have the file open in your text editor and in the browser. You can make a change to the code, do a save and then go to the browser and do a refresh and see the effects of your change. If your editor allow, you can undo the change and save, then refresh in the browser and you are back to where you started.
Now you can go into the code and add CSS to the end of the Atahualpa style sheet and see what happens. Once you get it the way you want, you can copy your changes to the 'CSS Inserts' option of the theme.
This is how I do it, not magic, simply a bunch of testing and looking at the code and playing with the CSS. Some people use FireBug, I like to do it this way since I can rip out vast sections of the code that don't affect the area I'm interested in. For example, if I am working on a menu issue, I remove the middle and footer, I don't need the side bars and posts etc. If I was working on a styling issue, I'd start deleting the style sheet chunk by chunk till I found the code that was causing the issue.