So, you have a requirements matrix then with readily identifiable markers? In which case, your testing is based around ensuring that you have satisfied the elements in the requirements matrix. Typically, you would do this by identifying the requirements that are in scope, in your solution, out of scope, not applicable. You also need to identify what parts of the system are affected by the requirements (hence the matrix), and mark these off using the criteria I've just laid out. Now, you know what is in scope and what is out of scope, you should be able to start mapping out what needs to be delivered in what order. I like to use a tool such as Enterprise Architect to link requirements to Use Case documentation, which will indicate what requirements are being satisfied. The traceability matrix you produce is a useful tool for your testing teams because they can ensure that the delivery is satisfying the requirements. This is a huge area, beyond the scope of a simple forum discussion, and it's why a company pays a good BA a lot of money; they take this type of thing in their stride. I will say that a good BA is a must; they will save you from falling flat on your face.
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