IPA: /ˈsɛpəˌrɛtli/
KK: /ˈsɛpəˌrɛtli/
In a way that is distinct or apart from something else.
The two teams will work separately on their projects.
Separately → It is formed from "separate" (from Latin *separatus*, meaning set apart) and "-ly" (meaning in a manner). The word "separately" means in a manner that is set apart or distinct from others.
Think of something being 'set apart' ('separate') and done 'in a manner' ('-ly') — that's why separately means to do something distinctly.