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!