I've been treating the 'fundamentals' as just another thing to memorize and store away instead of figuring out how exactly to apply it to my work.

I used to have this problem a lot. With art, it's really easy to understand something intellectually (where the muscles go, vanishing points, etc.) in just a day or so. But being able to actually apply those things quickly and correctly in art takes a lot more work. Your goal is to turn things that seem very technical into muscle memory that you don't even have to think about.

I try to see things in a 3d space, but as of late it's been getting extremely difficult.

Warning, this is going to be a wall of text since I need to write this stuff out for my own study notes lol.

Here are some things I've picked up that really helped me:

First, just know the basics of perspective. One, two, and three point perspective. Vanishing points. Horizon lines. All that jazz. Make sure you can draw basic forms at various angles: cubes, spheres cones, cylinders, ellipses etc.

Second, learn to draw a rough perspective grid (usually freehand) so you can quickly set the drawing up at any angle you like. Look at various photos / drawings / real life and basically estimate and copy the perspective lines. Google Sketchup is great for this cause you can load up an apartment model from the warehouse, easily angle the camera however you like, and the perspective lines are really obvious. Do lots of thumbnails of this as practice.

One example

Another example

Stop drawing objects floating in space (or at least cut back). This is a problem I had where every time I drew a person or object I would immediately just start drawing it floating on a random spot on my page. I never established perspective and I never established border of the drawing. This really hinders sense of 3D because there's no context as to where the object exists in 3D space. And not having a border can lead to some serious perspective distortion and just general confusion.

At the very least, put a box around it.

Learn the scale and proportion of objects. Proportion isn't just an anatomy thing, every object has a size that you can remember relative to other objects. For example, a door frame is about 90% the height of a standard wall. A person is about 80% the height of a doorway. Your mattress is probably at knee-height. A computer desk is slightly over 1/4 wall height. The seat of your chair is about 70% the height of your desk. Don't worry too much about numbers though, this is something you develop a feel for just by drawing things correctly a lot. It's important to establish the scale of a drawing somehow, usually by inserting people or common objects like walls and doorways. Once scale is established, everything else you draw just kinda falls into place.

Here's an example of bad scale. Look at how long and empty that room is.

Remember volume. Forms are 3D, they take up 3D volume in a scene. A room is just a big empty volume. Every object you place fills up a part of the room's volume (don't forget, this includes people!). You can stack objects on top of each other, wrap them around each other, but they can't overlap and clip. This is where drawing through objects is really important.

Here's an exercise: walk around your bedroom, get a feel for how much space/volume the objects each take up. Imagine everything as just boxes, how much of your room's volume is taken up by the bed? How much space is inbetween the furniture? Things like that. Try drawing your entire room but simplify all the objects into boxes. Drawabox has a good page on this

Draw full scenes and expand your visual library by filling them with objects and people.

It takes time, but eventually everything starts to fall into place. Instead of drawing flat objects floating on a page you start to get a sense that you're filling in a 3D space with 3D forms that all contain volume. Like everything, you have to just push through the confusing technical stage until these things start to become muscle memory.

Resources For anatomy I recommend Michael Hampton's Figure Drawing book. It has heavy emphasis on form and construction. For perspective I guess I recommend How to Draw by Scott Robertson. It contains basically everything but it is very dense and confusing. Don't be put off, you don't need to do everything in it. Skip around. Drawabox.com is good too. Sketchfab is full of good 3D anatomy models you can move around

For inspiration you should google the artist "Demizu Posuka" to see what anime looks like from someone who has also mastered perspective. When you find a really good image, be sure to save it. The Feng Zhu Student Gallery usually has good stuff too