Someone correct me if I'm wrong but I think you have 3 problems:
Your cube is not constructed "true" enough and therefore you are getting wonky results with the cylinder.
You are tilting some of the top ellipses away from the top plane of the box and not staying within the boundaries of your guides.
You are also not extending the top ellipse far enough into some of the corners
Perspective and construction can be so confusing and slow at first. You'll get there! I don't know if practice makes perfect, but I know you can definitely develop the "talent" for drawing. Good luck.
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@TessaW Thank you very much for clear instructions on how I might improve them, I think that's exactly what I needed! Also, thanks for the last two sentences. I thought that the fact that for me learning some basic concepts takes so long might be a bad sign, so thank you for the kind words and motivation.
I'll try to put your advice into practice as soon as I get back home and post the results here.
@TessaW I tried that and, although using vanishing points placed on the same horizon line helped (I totally ignored that there should be only one horizon), the ellipses still do not seem to match.
The top one seems right, but I think the reason why I keep failing is that the bottom one is always kind of skewed. I guess that the only thing I can do now is go back and practice drawing ellipses in one-point perspective. Or maybe it is okay to continue the course and hope that one day it will just "click"? 
Once again thank you for your advice, it probably saved me a lot of trouble with two-point perspective!
Without analyzing it too carefully, it looks like it may be about just extending the top ellipse further into those side corners. Getting those ellipses right can be quite tricky. Maybe someone else can chime in.
Something else I'm noticing is that you aren't quite nailing where the halfway marks are on the planes of the box. I don't know if this is affecting the ellipses of not, but I thought I'd point it out. Jake sort of freehands the major and minor axis's in the course, but a way to find the halfway point of the planes are to draw lines from corner to corner, and drawing a line through the center point of the x to the vanishing point:
(image by Scott Roberston)
I would say 1. Sometimes you may need to supplement a course you are taking with other sources. If I'm not understanding a concept, I will look toward one or two more places to help me understand a concept better. The other source may explain it in a different way that really compliments and rounds out what I'm learning from the original source. I would also say that 2. It's absolutely ok to move on and you can always revisit concepts. In my opinion you sometimes have to move on, experience other things, take a break, and concepts will click later down the road.
I know @davidhohn rolled out a perspective class recently- it looks really good. That maybe a good place to either reinforce this concept right now, or go to in the future after you finish the How to Draw Everything course.
Some thing to try might be to draw the bottom ellipse first, extend the sides up, then try to do the top ellipse, making sure to hit those points.
@Kiddo TessaW nailed it with her answer. Especially about extending the elipse into the corners. The top ellipse on your cylinder is closer to the horizon line and will therefore be more flattened or squished than the ellipse on the bottom.
@TessaW @marshallx Thank you both for your feedback and advice! After some practice, thanks to your tips and guidance I finally made it. It's not perfect, but comparing to the pictures I posted yesterday I can clearly see there is an elliptic light of hope somewhere far ahead.
Best community ever. If it wasn't for you, I would probably lose my patience and get frustrated.
@Kiddo Wow, great job pushing through, it's looking really good! Eventually you won't have to draw out these boxes in order to do cylinders, but doing these will really build a good foundation for you. Well done!
@gavpartridge I thought so too, but Jake advises against it, I guess it just gets more difficult to get rid of the ruler in the future if you start with it in the beginning.
@TessaW Can't wait for this to happen!
@Kiddo said in Ellipses, cylindres, 3D shapes [beginner]:
@gavpartridge I thought so too, but Jake advises against it, I guess it just gets more difficult to get rid of the ruler in the future if you start with it in the beginning.
In art there are many paths to the same location. I can say from experience that it is not hard to ditch the ruler.
Not saying that Jake is wrong. His method worked for him. But I would second the advice to start with a ruler and a nice sharp pencil.
@TessaW @marshallx Thank you both for your feedback and advice! After some practice, thanks to your tips and guidance I finally made it. It's not perfect, but comparing to the pictures I posted yesterday I can clearly see there is an elliptic light of hope somewhere far ahead.
Best community ever. If it wasn't for you, I would probably lose my patience and get frustrated.
