What is the safest way to upgrade to 64-bit?

The warning message is alerting you that there are #2 bit apps on your Mac. They will stop running after the upgrade to Catalina this fall.

In order to discover which apps are 32 bit, goto http://osxdaily.com/2018/03/06/find-32-bit-apps-mac/

Macs are already 64bit. They have been for 10+ years. You will have to update any 32bit apps if you are planning on running Catalina in the Fall.