I have already written my entire thesis in LyX. But my university has a fixed LaTeX format in which I've to turn my thesis in. Kindly advise.
The question is general so is my answer.
Assumptions - less likely
you have finished your document (e.g., thesis) and will not change your document much;
... AND ...
- you know roughly about LaTeX, BibTeX, Makeidx etc.;
Suggestion: The fastest way to use the required LaTeX styles is to export all your LyX documents to LaTeX. It might be safer to create a new directory and copy all the LaTeX file, pictures, and everything what you need to build your PDF there. Then edit and adjust my LaTeX such that the required template is used.
Warning: If you have to edit your document later on, you need to edit the LaTeX file directly or it might be error-prone to re-export your changed LyX document .
Assumptions - more likely
you have not completely finished your document and probably will have to edit some parts;
... OR ...
- the LaTeX template is simple (e.g., just a style file and not a class file);
Still you need to know about LaTeX a bit. Maybe read "A (Not So) Short Introduction to LaTeX" or similar...
Suggestion: Copy the settings from the main LaTeX file of your LaTeX template (and possibly further configuration files) into the LaTeX preamble of LyX. Note the LyX provides quite a lot of setting via "Document setttings". Hence, instead of copying code to the LaTeX Preamble use the corresponding LyX settings.
Note that for LaTeX files of your LaTeX template that hardly need to be changed by you (for example, a LaTeX file which contains the title page) you can just include them into LyX by "Insert > File > Child document" (then use "Include" or "Input" as was used in the LaTeX template).
You can also try to import a LaTeX file into LyX via "File > Import". If it straight compiles afterwards then fine. But be aware that quite concealed errors can occur sometimes.
(It will get more difficult when your LaTeX template provides non-standard environments that are to be used for things like tables or figures.)