If you need to modify parent affiliate or you want to manually add new affiliate and set it as a child of some of your existing affiliates, you need to follow these few steps.
First of all, you should check your signup settings - if you set parentaffiliateid to be hidden, you need to temporarily set it to optional (or mandatory). You can find this setting in Configuration> Affiliate signup> "Fields" tab
Do not forget to save your changes.
Now, in affiliate details you can set/change parent affiliate. If you want to add new affiliate, click "Add affiliate" button in Affiliates> Affiliate manager. If you want to modify existing user, click on pencil icon in Actions tab in Affiliates> Affiliate manager
Now, navigate to Details tab and here you can set/change parent affiliate a drop down menu: