Question: So im about to start developing a responsive site and was wondering if i should use media queries to modify one element, or have multiple elements and just hide them in and out... Thanks

Ex. one nav and modify it based on resolution or 3 navs big, med, and small.. and just hide them based on resolution

Answer: 
It's better to have one element and modify the style via media queries unless your content is so drastically different that having one element becomes kludgy. In which case, maybe you need to ask yourself why your mobile content is so very different than your desktop.

I'd suggest starting here: <http://alistapart.com/article/responsive-web-design/>
Media queries are definitely the way to go :). Else it will probably get pretty messy.