First of all many thanks to all members especially to Mr Stefan and Mr Johannes for their help. I really learnt so much from here and I am about to finish my thesis.

There is still a little problem that I have in the bibliography part. I am using Chicago style of referencing but I don't know if I should write by references in the main file or is there any special file for it? (the template has files for chapters and appendices only)
Secondly, if I write them in the main file, I don't get the bibliography in my table of contents.
An example will help me a lot.
I would really appreciate your help in this regards.
Regards,