how to upgrade from intel to silicon manually

The Setup and Migration Assistant app tools — those are basically the same tool, though the former runs at first startup, and the latter can be run later — can select what is transferred.

Transfer to a new Mac with Migration Assistant - Apple Support

Apple has a related tutorial here:

https://it-training.apple.com/tutorials/support/sup090/

If you want to go fully manual, then you’ll be learning about where macOS keeps its various giblets.

I don’t see any reason not to go fully manual here, as you’ll learn much about your environment and about the tooling. You can then reset the new install if needed, and start over fully, and can then use the automated migration tools.

Manually moving your data is not wise, it is best to follow the directions below. Then to get rid of the data you do not want on the new machine, simply move it to the Trash and empty it. The ONLY other method is to copy and paste, which is slow & mistake prone!

·       Always connect your old Mac's Time Machine External Hard Disk prior to startup, this will allow a migration from your TM backup and it will be dead simple! When you start the new Mac for the first time it will startup Setup Assistant (SA), SA will get to a point where it asks if you are migrating from another computer, select Yes and follow the on-screen prompts and it's done! It is that simple! This is the easiest, quickest and most reliable method to migrate from the old Mac to the new Mac is to simply connect the old Mac's Time Machine External Hard Disk to the new Mac using a USB cable before you turn on the new Mac. 

·       NOTE 1: You will likely need a USB A to USB C adapter, you can find them on Amazon for $10 or less.

·       NOTE 2: If you have already done SA on the new computer then simply connect the Time Machine External Hard Disk using a USB cable and launch Migration Assistant (MA) which is located in Applications - Utilities - MA. Then follow the on-screen prompts.

·       The ONLY difference between MA and SA is MA will create a new user account that you need to log into.

Both SA and MA migrate applications (not 32 bit apps), data files & settings. They do not migrate Mac OS itself. Some professional apps such as Adobe and Microsoft apps may require re-installing their apps as they will not allow them to be migrated. As long as you kept the security keys for installing their apps, it is not an issue. 

Finally, never EVER use Wi-Fi when doing Setup Assistant or Migration Assistant. Why, it simply fails in most cases. Please read and follow the directions in Setup Assistant and Migration Assistant. If you do not have a Time Machine backup of the older Mac then create one! If you are not aware of Time Machine, please read Back up your Mac with Time Machine and finally if you need an External Hard Disk to use as a Time Machine External Hard Disk then many experience users on these forums prefer the OWC Mercury Elite Pro due to it's reasonable price, high level of quality and ease of use. 

I agree with rkaufmann87's recommendation of not manually moving data. You would lose all of your application activation codes, passwords, settings, etc. If you haven't saved them somewhere it could be difficult to recovery them from the developers.

If you decide to use Setup or Migration Assistant before you do so uninstall any "cleaning", "optimizing", "speed-up", anti-virus or VPN apps on your Mac. They are unneeded and can adversely affect system and application performance.

Not really. Your mail and contacts are set when you add your email account. Music and photos have contained libraries or can be downloaded from iCloud (if you sync with iCloud and subscribe to Apple Music or iTunes Match)