Well integration testing does not have any methodologies.

Here we are testing to see if all the modules have been integrated perfectly or not.

Taking for granted that all the modules are throughly tested and are free from any show stoppers and high defects............ My system is good to go for an integration test.

I create scenarios which take me through all the integrated modules or just a few of the modules.

The test lead / manager should sit with the business user and or an analyst to work this out.

A Person with business experience should be of great help in creating the test data even before you create a scenario.

Needs:

1) Explain the Test Data.

2) Exp[lain the Scenarios.

3) Explain the testing process - How you are going to test defect tracking process smoke testing blah..blah...

4) Qa Sign off.

All these should be explained in a Very detailed and Specific test plan and you should be good to go.

Its just another testing effort with the tester wearing the Business User shoes.

Forgot to say one more thing These integration test scripts need not be testing the whole functionality mentioned in the requirement documents. A business user's input on it on categorizing what is more important or most commonly used functionalities should narrow your scenarios.

Question to me: If we are not testing few functionalities how come the Integration testing is complete.

Answer: To me the test data and the scenarios are pretty much what the business users face. so we are covering what kind of business that is done every day. For the rest of the functionality You did a functional test and you are confident on the working of the functionality? aren't you? if your answer for those questions is No then we have problem or else we should be good.