Learn in-depth about airplane operations Currently seeking a book or manual that teaches a civilian how a cargo aircraft operates and what it's pilots do, say a 787. Preferably a high-level overview at a per flight phase:


Pre-flight: Flight planning, aircraft checkout (airworthiness), maintenance checking, taxing, ATC communication, etc
Take-off: What do pilots look at during take-off: engine parameters (torque?), airspeed, etc.
Cruise: What do pilots moderate during cruise? What are they doing to prepare for landing? 
Landing: Again, what parameters are they looking at, and how often are they looking down? How and what are they communicating to ATC?
Post-flight: What happens to the aircraft? What maintenance is done on the aircraft? What are they doing while they await instructions from ATC? What reports are looked at.   


I understand that this is a lot of information to ask for from one book but I am willing to do a lot of reading, from various sources. Any help in answers these questions would be greatly appreciated as well. Young engineer in the aerospace industry and I'd like to learn more.
I'm not aware of any official resources which present all that information in a concise way, but to get a general idea of the operation of a modern civil passenger aircraft you can refer to the manuals provided with flight simulation add-ons. As opposed to the standard aircraft contained in most flight simulators, these payware models are very accurate and highly complex.

Next to the complete manuals, each aircraft typically also contains a tutorial flight manual, where all the steps necessary for the operation are shown in detail (100+ pages each). Here are a few examples:


787: http://qualitywingssim.com/files/ultimate_787_collection/docs/QualityWings%20-%20Ultimate%20787%20Collection%20Tutorial.pdf
A320: https://www.aerosoft2.de/downloads/a318-a319/Aerosoft-Airbus-A318-A319-Vol6-StepbyStep-EN.pdf
Some other Boeing aircraft (PMDG): https://www.precisionmanuals.com/pages/downloads/documentation.html


If you're specifically interested in ATC communications, you can for instance refer to the IVAO documentation about IFR phraseology: https://www.ivao.aero/training/documentation/books/DOC_IFR_phraseology.pdf

Remember that these are NOT official documents, so they are not suitable for any real world use. But in my opinion they are the easiest way to get an idea of aircraft operations. At least that's how I learned it! It has helped me a lot in my Aerospace Engineering studies.