Abstract, Preamble, Acknowledgements and Introduction all in Thesis, how to order them?
(I expect people will tell you to consult with your advisor, and you should, but on the other hand I think most of this question does have a right answer, so I've tried to give it.)

It sounds like you have three main parts to your thesis: the management plan, the guide, and the database. So your thesis should have three main sections (if one of the three is an appendix, that's okay), and there needs to be a single introduction that ties together the entire document. One of the things this introduction should do is explain the organization of the rest of the thesis.

If you want to write a more specific introduction to one of the sections, it should go at the beginning of that section. You can call it "Introduction to Section 2" or whatever. Using the word Preamble confuses the issue, and it also sounds pretentious.