Well you learn it over time with lots of hands on mostly on your lab.

If you can conceptualize router on the stick I think the same process apply here.

For router on the stick when you split the interface to different sub interface one physical interface gives your three logical interface. The logical interface is virtual but behave the same way a physical interface work a lay man language though.

Logical topology is what give you an ideal of how the data move in the network which means it may data path may inter an interface several times before reaching its destination.

You can do some google search on "mastering converting logical topology to physical topology."

You will be amaze what result and explanation and practise you are going to get.

But know that with practise come perfection.

Cheers.

Like adecisco said, all it takes is basic understanding of Layer2 and Layer3 and some experience. It's one of those things that will become natural after you have seen enough of them whether from books or Cisco docs.
From the given logical topology, there are countless of way to come up with the physical. You can even connect the whole lab on a single switch just by separating routers in different VLAN.