Hi, I’ve been struggling with this since a few days ago, so let’s see if you guys can point me in the right direction. 
With my basic knowledge I’ve been constantly confronted with situations where some bit of geometry ends up inside of itself…
I haven’t been able to get rid of the intersecting bit. What would be the best way to solve this?
Thank you in advance!
You probably want to do stuff, for which you need more knowledge explained in upcoming lessons. So be patient.
That said, instead of creating a single object containing everything, which is a solution. There are other tools to use. For Blender, it is NO problem to have intersection bits! It’s part of the 3D design toolset.
Only render problems can occur when faces meet at the same location and angle. Intersecting faces then generate a strange texture/material.
So what to do …
All these solutions need more knowledge of Blender. The modifier is the easiest way. The sculpt tool the most difficult one. I would advise not to choose that process.
Manual is the most flexible one. But as I stated earlier, intersecting meshes are not a problem. Try it out and render the scene.
Intersecting geometry is fine even animating it can be if you are mindful of it although we tend to try to avoid it if we can just for sanity.
The things to mainly watch out for is faces occupying the same space as time travellers know two objects of amtter cannot occupy the same location in time and space else things just go badly
We call this Z fighting which is where they try to render two faces in the same place and its fighting to render which one on top.
As mentioned though in these cases its not an issue.
Internal geometry though like if you made the handle from a torus and left half of it inside the cup per say then that would be wasted as its still rendering something that you would never see (Realistically it would be seen on the inside but for this just imagine the cup is sealed object)
Hope this helps and more is coming up
Thank you for your answer!
Yes, I figured as much. But as fellow 3D artists, I’m sure you can understand that sometimes we want to figure out certain hurdles we find along the way, even if not by acquiring the in-depth knowledge that would help us understand the whole picture, but by simply solving the specific case at hand.
Having said that, I find your answer and @Marc_Carlyon 's very satisfying and enlightening. I sometimes become too much of a purist and try to find elegant solutions. ^^
Thank you again, and I’ll come back further along the road to see if I can leave my own answer to this.
I had this problem too in the beginning. As an engineer, I want to look at a problem in a scientific manner. To be precise.
Besides that, Blender can calculate real physics, but it’s also a creative tool. Where physics are applied but in a very ‘loose’ manner.
Don’t give up and have fun!
Thanks!
Don’t worry, this forum is not getting rid of me anytime soon. I’ve got tons of questions / frustrations / exciting things to bring here. 
Indeed the important if not the most important thing is to have fun, Thats where the creativity happens.
Happy to help here on the forums or in discord as well
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