For the Corporate Marketer package, Lead Scoring is managed in the Lead Scoring section (Administration->Lead Scoring):
For all other packages, Lead Scores for Phone Calls can be adjusted in the Phone Call Notifications workflow. This workflow is used to manage how leads are distributed when a Phone Call comes (or is made). The workflow can also be used to update the lead score before the lead is sent to sales.
Navigate to the workflow (Automation->Workflows), click the pencil on the far right of the "Phone Call Lead Notifications' workflow:
Once inside the workflow editor, drag a Decision step onto the canvas.
To understand the context of the call, build a query in the decision widget to inspect the incoming call. For example, you may be interested in what pages were visited, where is this contact, have they called before, etc. After you context has been determined, drag a Adjust Lead Score action onto the canvass:
Now you can adjust the lead score based on your context. Select the connection wire connecting 'Incoming Call' and "Has Contact Manager', click delete in the properties box. Insert your steps into the workflow.
You can add as many queries and adjustments as you want within this workflow.