I was drawing with this program for awhile now and having yet another problem with it. See I'm trying to shade my drawing in with the pen tool and for some reason my inkscape thinks it's on the drawing layer which is lower then the coloring, even if it's on the every top layer, I'm starting to think I need a new program if this nonsense keeps up.

Can you share a screenshot or the file you're working on, with a description what exactly you're doing? I'm not sure I can follow.
You can select the layer to draw in in the layers dialog.
You can set a blend mode for layers (but you probably don't want one). Some people accidentally set one and wonder why things look strange.
You can change the opacity of the layer, the object, or the stroke or fill of an object. Maybe that's what you mean by 'fazing through'?

It sounds like you might be misunderstanding some things. If you could provide an SVG file, and describe each problem that you're having (which the SVG file demonstrates) we can probably help you to understand.

Transparency can be very confusing. It can look just like an object on a lower level is visible through an opaque layer in between, when it could be you're drawing on the upper layer with some transparency, and there's a layer blend mode in effect. And if it's a complex canvas, perhaps in a simulated 3d drawing, where you might have 6 or 8 duplicates stacked up to provide highlighting and shading.... Well, things can get pretty crazy sometimes, haha!

Darn it, Moini! That's some kind of radar you have!

I warn you though it's weird nsfw https://www.dropbox.com/s/pee4i9qvz2s7w6w/BBtest.png yeah how do I make the shading triangle go on the colors and not behind them is the proper question. Though mind telling me how to share the SVG file?

If you're using dropbox, the SVG file can be shared the same way. Upload, make available publicly, post link here.
(you want the black triangle that is currently behind the blue woman figure above it?)

https://www.dropbox.com/s/ns5m0om75i9s4 ... m.svg?dl=0 Thanks and yeah I would like the triangle on the blue woman not in between the colors and lines.

The problem is that some of your objects aren't on a layer at all. They are in the 'root' of the document, and because they come last in the SVG source text, they are at the top of the drawing and cover everything that is in the layers below.

I can't tell you how they got there (perhaps you've started from a preexisting SVG created by a different vector graphics editor?), but you can fix by moving the other objects into their correct layers. Select, right-click, move to layer.

Background info:
Layers don't exist in SVG. They are a concept in Inkscape, emulated by using SVG groups, that have an Inkscape-specific attribute, so Inkscape will recognize those groups as layers. Other programs don't have those. In SVG, you can have objects directly in the outermost element, in Inkscape, usually you will have a group in that element, which is the first layer.

Edit: to find things like these out by yourself, give special attention to the status bar at the bottom of the window.

I also noticed that you seem to be using the bucket tool a lot, creating ugly seams between the outlines and the fills. You can fix by doing Path -> Outset (the step can be adjusted in the settings).
Or you can try using the Bézier tool, and add a fill to the shapes you create. To get the dark contours, you could use the power stroke, or you can just add a stroke to your filled shapes.

Along with Path Outsets to solve the gap problem with Paint Bucket, there's an option on the control bar called Grow/Shrink. So you can set it for + 1 or 2. Or just experiment to find the value which works the best with each particular object.

In addition to keeping an eye on the status bar, as Moini suggested, don't forget about Help menu > Inkscape manual. If you have some extra time, you could try Help menu > Tutorials > Basic, Shapes and Advanced. Don't worry, every though it's called advanced, it really is an introduction to path, and entirely appropriate for beginners. The other tutorials are good material too, but those 3 are the main ones for beginners. Anyway, by going through those tutorials, you can begin to learn the correct terminology, which will make it easier to use the manual.

Although we're still going to be here, if you need help
It's just nice to be able to solve your own problems, and not have to wait for us to answer.

Thanks for the help, I'll see what I kind do with new info.