What is the difference between architecture and structure in computer science?

Judging by your question I can try to answer with the following: I believe what you are referring to would be the Computer's "Form Factor" that will determine what parts and/or components you can install in a particular CPU case. The form factor does control how you would organize the parts, it dictates the architecture, and what hardware you are allowed to install. Some form factors are:AT/Baby AT, ATX, LPX, BTX, NLX. The most common used today would be ATX.

To over-simplify things:

Computer Architecture is the idea which specifies how the different parts should work together, and how they should work individually. Computer Organization is the plan for implementing the ideas in the Architecture. The Computer Hardware is what results from implementing these.