Heres a new logo Iam workin on for a client on oDesk.

I wanna make the staff a bit more shiny and shadowy, give it more depth sorta. how can i do it with Photoshop??

I like the image the way it is.

It is nice as, is but burn & dodge tool will work good for adding a "metalic" look to it which is what I assume you mean by "shiny".

Gradients and over layers of white to translucent. You know the deal.

I would use a little darker shade of blue on the staff and use the 3D Effects Inner Bevel Tool. However the logo looks really nice the way it is.

If I wanted to make the staff go through the bottom part of the '5', how do i do that?

You could erase part of the staff on top of the 5, not sure how great that would look, although it could be done. What I would do is break the graphic/logo into pieces and work with transparent layers. One layer would be the staff, another layer would be the Top Medical, so on.