If you have windows XP or whatever, it will only replace the files that are included. For example, your original folder contains files A, B, and C. The mod replaces files A and B. If you drag your new folder, and accept the replace prompt, it should only replace files A and B and leave file C alone. Understand?
Specs: AMD Phenom II 940 3ghz, ATI Radeon HD 5870, 4gb DDR2 800, Windows 7 Professional x64