My suggestion is writing it directly using LaTeX files.
Nonetheless, said that, unlike many thesis templates, in this case
main.tex do not use a custom document class but the standard
book that is already supported by Lyx without any special configuration.
So you can File > Import > LaTeX (plain) ... > select
main.tex. This will make
main.lyx as well as lyx versions of all the subdocuments.
However, the imported file will have some problems:
1. Conflicts between the imported preamble and own LyX settings for the document. The solution is remove from Document > Settings... > LaTeX Preamble what could be fixed in other sections of Document > Settings....
For example, in the original
main.tex file, this lines:
Will be traduced by LyX in this LaTeX source:
Beside setting defaults margins in
geometry, this is wrong mainly because the
croatian option cannot be passed two times to the
babel package. But you can remove both packages from the preamble and configure them through the LyX interface to produce this:
That is essentially the same that the original .tex file.
2. Many LaTeX code remain as Evil Red Text boxes (aka ERT boxes or TeX Code boxes that you can insert with Ctrl+L ).
Generally the ERT boxes are not harmful (the file is still compilable) but annoying. In this case, many of these ERT are LaTeX comments that you remove safely or convert in yellow notes. Others are commands as
\tableofcontents that you can replace easily by Lyx objects as Insert > List/ToC > Table of contents and some others could be LaTeX code that is better maintain "as is" since you cannot (or you do not know) replicate through the GUI of LyX (for example, the
titlepage environment). If unsure, left the ERT boxes!
3. Imported images are too big on the screen. This is a minor problem easy to solve: Right-click on the image Settings... > LateX and LyX options > Scale on the screen (%) > try with a 1-10%. The image size on the PDF is not modified by this setting.
4. Conflicts inherited from converted sub documents. The conversion of the main file is not too hard but debug compilations errors due (for example) to a
tabularx environment infested with dozens of ERT boxes in a included subdocument will be a nightmare even for experts. Simply avoid these conflicting example subdocuments until you have a compilable main file. Then start including simple subdocuments with only some text. Remember that LyX cannot produce any type of LaTeX code, only the most common commands and environments, but you always insert unknow code for LyX as long as you use the ERT boxes, and when needed, packages/definitions in the preamble so LaTeX can understand these ERT boxes.
So, after some cleaning, your
main.lyx could be some like this: