If your work includes experiments, case studies or software prototypes, it is also useful to number or label these, so that it is easy to unambigiously refer to Experiment 3 or prototype P4. Talking about 'this experiment' or 'the improved version of our prototype' quickly becomes ambiguous.
The same goes for list of (dis)advantages, problems, etc. Here numbering or labelling can also be useful too. To prove the point: this checklist is numbered so that I can easily point out to students that they forgot to check item N.
That way it is clear where new paragraphs start.
You can also have vertical white space between paragraphs,
but then you have to make sure you do it consistently everywhere.
Indenting the first line of a paragraph is default
LateX behaviour that is best left unchanged.
An advantage of indenting the first line of each
paragraph instead of having vertical white space
that you can then use vertical white space to group several
related paragraphs together, as is done in this paragraph.
(Here the paragraphs are very short, so it looks a bit silly
maybe, but usually paragraphs will be longer.)
For academic publications this must include the conference or journal name and the publisher (e.g. ACM, IEEE, USENIX). The publisher is useful information as it can provide an indication of the academic reputability and rigour of the peer-review process.
Include the names of all the authors, unless there are more than a dozen or so and it becomes very awkward. The full list of authors can provide useful information. For example, if two papers make the same claim it is good if the reader can see if the two papers are not by the same authors but with a different first author. And if some paper claims that tool X is great it is useful to see if the people who made tool X happen to be co-authors of the paper. (The Biber tool for BibTex by default only lists the first author, but you can set maxbibnames to a different value than 1.)
It is perfectly fine - and it may in fact be necessary - to refer to so-called grey literature, such as personal blogs, white papers, articles in online magazines, newspaper articles, etc. But it should be clear what kind of source it is and who wrote it: is it by some reputable expert or (an employee of) a institute or company that has expertise or experience? It is even possible to add citations to conversations or email discussions you had with people, as 'personal communication'.
The note field in BibTex is useful to include information such as 'personal blog' or 'company whitepaper'. Of course, you can also provide such information in the text at the place where you cite the source. For example, if you cite a company whitepaper for claims about the quality of a product by that company it is good to point out in the text, so that readers know to take these claims with a grain of salt -- and so that the readers (especially the people grading your thesis later :-) know that you as author are aware of this.
When you referring to, say, the github page of a software package it is fine to stick that URL in a footnote, as the author and publication date are not that relevant. Of course, the version number of the software may be relevant to mentions, but a full citation is usually overkill. The same goes for references to the homepage of some organisation.
It may take a while to get this right. A useful trick is to start every chapter (or larger section) with one sentence or a short paragraph describing what the chapter is about, what the various sections are about, and how it is related to previous chapters and/or the ones that follow. It can also be useful to look at your table of contents one in a while to see if the structure is clear from that.
Whatever you do, having a chapter titled 'Research' is never acceptable, even if the LateX template you have been given has such a chapter.
At secondary school you may have been taught to vary the terms used to refer to someone or something, e.g. to refer to 'Mary' as 'the girl' or 'the student' once in a while, so that you do not end up with boring prose. But for technical terms in scientific literature you should avoid synonyms like the plague as it quickly causes confusion.
Define concepts that you use once, in the right place, and then stick to the same name for that concept throughout your whole document.
Terms like 'the application', 'the implementation' and 'the software' that quickly become unclear as there are usually several applications and lots of pieces of software around. Also terms like 'the framework', 'the platform' and 'the system' quickly become confusing. Using the names of applications, systems and platforms can avoid a lot of confusion.