Suppose package name is ATOM_PACAKGE

Step1 - press "Win+R" and type "cmd";

Step2 - cd .atom/packages;

Step3 - find url of ATOM_PACKAGE in GitHub;

Step4 - git clone $url(of ATOM_PACKAGE);

Step5 - cd ATOM_PACKAGE;

Step6 - apm install;

Step7 - Done!