Color Changes Not Working in Menus. +Menu help.

I have read multiple posts regarding the color changes and have yet to find my fix. I can not get the default “blue” to change in many of the buttons for menu and search boxes on top or right side navigation menus. I also was trying to change the bottom thin blue horizontal line color. I would like to customize this for my site and other future sites I may build with this theme. I have tried to customize some of the css. & php. files but with no luck. Had to revert to the originals. Please help with instructions of what to do. I prefer to do this myself since I will need to do it in the future for other sites as well.

Also, I cannot get the site menu to display which shows the pages I have created. I have attached a jpeg. to show this.

Thanks.