How are orbitals arranged in an atom? I'm really confused about the ideas of orbitals, shell, subshell and most importantly how are they arranged in an atom? According to my knowledge orbitals are region having highest probability of finding electron.When I saw this video, I was more confused than ever.
Lets say for a second that I know the placing of orbitals (as shown in the video), but what does it actually mean, i.e how are the electrons actually moving and stuff?
Can anyone also help me visualise an atom (i.e electron's trajectory/movement and other stuff)?
 A: 
Can anyone also help me visualize an atom (i.e electron's trajectory/movement and other stuff)?

The basic help is to emphasize that electrons and atoms are quantum mechanical entities, not classical particles with continuous trajectories as functions of (x,y,z,t).
Quantum mechanics means that at the microscopic level what can be seen and measured is an instance in (x,y,z,t) in a calculated probability distribution for a particular orbital. Orbits belong to planets and the semiclassical  Bohr model, which does  predict orbits in one to one correspondence with the theoretically correct quantum mechanical probabilistic orbitals. Here for the hydrogen atom, which is simple:

What does this plot mean? It means that each dot is the space time location where a single  electron is found when an experiment is done. There is a definite locus ( around the semiclassical Bohr orbits ) but the probability of finding the electron at a specific (x,y,z,t) is given by the $|Ψ|^2$ of the corresponding hydrogen wavefunctions. (which were used to make this plot).
There has been experimental confirmation of the hydrogen orbitals


What you’re looking at is the first direct observation of an atom’s electron orbital — an atom's actual wave function! To capture the image, researchers utilized a new quantum microscope — an incredible new device that literally allows scientists to gaze into the quantum realm.

Here are more complicated molecular orbitals,
 
In the space where there are no electron orbitals the attractive positive forces from the nuclei can dominate , thus  atoms and molecules can attract each other and fit LEGO like into large structures
The more electrons an atom has, the more levels are occupied. In hydrogen when not excited  only the lowest orbital is occupied.
A: 
According to my knowledge orbitals are region having highest probability of finding electron.

Yes, you're correct.

Lets say for a second that I know the placing of orbitals (as shown in the video), but what does it actually mean, i.e how are the electrons actually moving and stuff?

The video simply demonstrates how the orbitals are arranged in an atom. It means how the electron clouds are placed around the nucleus. While studying atomic structure, we first study each of the orbitals and their characteristic. Now, this video shows the arrangement of orbitals around the $Sc_{21}$ nucleus. Note that electrons will move in only the shells as per the configuration of the atom. For example, the configuration of $Sc_{21}$ is:
$1s^2 2s^2 p^6 3s^2 p^6 d^1 4s^2$
So, electrons will only be found in these shells. The other shells of $3d$ are also present, but they're empty.

Can anyone also help me visualise an atom (i.e electron's trajectory/movement and other stuff)?

You just have to understand that the electrons are moving in their orbitals, and then these orbitals are placed around the nucleus. There's nothing more to it.
You cannot definitely tell the path of an electron, and that is why it's the quantum model. You can only tell where the probability of finding an electron will be maximum.
A: It might help to visualize things to not consider the electron as a particle. It is better to se it as a wave when in the orbit around the nucleus. The orbitals then are where the wave is strongest, sort of where the "sound" is heard strongest (if you sort of could "hear" the wave). It is possible to "hear" the electron far out of its orbit, but much weaker, ie lower probability.
The duality of the electron as both a particle and a wave is demonstrated by the double slits experiment. This duality is one starting point into the strange world of quantuum mechanics. The quantuum world is very different from the macro world we know, described by mathematics and verified by a lot of experiments. In order to calculate the orbits you have additionally sprinkle on a bit of special relativity which is a great subject in itself.
 https://en.wikipedia.org/wiki/Double-slit_experiment and   https://en.wikipedia.org/wiki/Special_relativity
