maybe a pic will explain better
take a look

http://ourworld.cs.com/throbem/shot.jpg)

how come that that part of my map is able to be seen across the sky texture, and is there a way to fix that?

It's a vis thing, we've covered it before.

When you stand in the bottom area you're standing in a node that can see a node behind the skybox so it gets rendered.

It doesn't matter if the skybox is in front becaue the skybox gets drawn behind everything else that you can see according to VIS.

If this wasn't a VIS compile (i.e. you just BSP'ed it)...try doing vis as well and it may fix. Otherwise you gotta look into fixing up the vis data.