You already did the most important part in my opinion: before using LyX, you should learn LaTeX well. You might find some replies useful on this thread: What is the difference between LyX and LaTeX?
Yes, you can use custom LaTeX packages. You can load them in the document settings in the LaTeX preamble. You can also load them through the creation of modules (see customization manuals). Similarly, you can use LaTeX commands by using ERT (Insert > TeX box).
The most important thing to know is that you are delegating a lot of things to LyX, and if you want full control, you should just stick with LaTeX.
I highly recommend the LyX manuals. They are dry, not fun, but we try to keep them up-to-date and they have a lot of useful details. Specifically, if you want to add support for LaTeX commands, or packages, that are not supported by default in LyX, you'll want to work your way through Help > Customization (but start with the other ones first).
Another important thing to know is that LyX is not a good choice if you are planning to work with someone who does not use LyX. Either both use LaTeX directly or both use LyX.
Another thing to know: join the lyx-users mailing list: https://www.lyx.org/MailingLists. You're welcome to ask LyX questions here on tex.se, but I think you'll find the list helpful (and friendly).
Another important thing to understand is LyX's file formats. For example, if you create a .lyx file in LyX 2.4.0 (which will be released in the coming weeks) you (and your coauthor) cannot open that .lyx file in 2.3.6, for example.