Hi,
today I will show you how % Complete is calculate on Summary Task level, and on Project Level as well, using Microsoft Project for the Web!
First, I will create one simple Project:

Firs three Tasks are connected, and second three Tasks are not connected at all. Now I will say that Task 1, and Task 6 are 100% completed:

As you can see, Summary 1 is marked as 50% completed. The calculation is simple: Task 1 has 3 days Duration. All Tasks under this Summary Tasks has 6 days duration (Task 1 = 3 days, Task 2 = 2 days, and Task 3 = 1 day, so Total 6 days). Now, 3 days (Task 1) / 6 Days (Total) = 50%
Similar, Summary 2 is marked as 17% completed. The calculation is simple: Task 6 ha 1 day Duration. All Tasks under this Summary Tasks has 6 days duration (Task 4 = 3 days, Task 5 = 2 days, and Task 6 = 1 day, so Total 6 days). Now, 1 day (Task 6) / 6 Days (Total) = 17%
Now I will click on My Project, and I will see:

Project % complete is 33%. Total Duration of all Tasks is 12 days! Now, Task 1 + Task 6 = 4 days duration. And, then Calculation is simple 4/12 = 33%.
Be aware of Milestone! It has 0 days and it brings 1 %! I will mark all Tasks as 100% completed, except the Milestone:
As you can see, If you do not mark all milestones 100% completed, even when all other Tasks are marked as completed, Summary Tasks, and Project as a whole remains 99% finished, and you do not want that.
Regards!
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About Nenad Trajkovski
Location: Zagreb, Croatia
Occupation: Project Manager
Interests: Project Management and MS PROJECT
He was born in Zagreb, Croatia at 1963. After completing his college he started working on projects in different business areas (banking, manufacturing, automotive industry, distribution, oil companies, etc.) developing and implementing ERP systems into different companies. He has got a lot of experience working with people in different business processes and also possesses great knowledge in information technologies and financial services. Today he works as a business consultant, adn Project Manager in PERPETUUM MOBILE d.o.o. Zagreb. He is a regular lecturer for Project Management in MS Innovation Center in Varaždin, Logosoft Sarajevo in Bosnia and Herzegovina and SEAVUS GROUP in Skopje Macedonia. He was named the best lecturer of WINDAYS 2008 while his lecture was also voted as the best. In addition, he was in TOP 10 lecturers at the MS SINERGY 2009 and MS VISIA 2009, 2010. Shares first place as the best lecturer of KulenDays 2009 and 2010 and PMI Conference 2009 in Zagreb. He is also a regular lecturer in the MS Community. He is a Certified Accountant and a PMP (Project Manager Professional) and a PMI-RMP (Risk Manager Professional), MCP, MCT, and Microsoft Certified Technical Specialist - Microsoft Project 2010. From 01.01.2012 awarded with MVP (Microsoft Most Valuable Proffesional - Microsoft Project)!