adding to the good points above.
Masters’ dissertations vary in length/form but can contain all of the structural complexity of a PhD, albeit in a shorter document.
The think all too many students (and their advisors) overlook is whether the awarding organisation has a defined format for the dissertation. Be prepared for the fact that such guidance will likely be out-of-date or incomplete, but it’s a start. Importantly, you can gauge whether your chosen writing tool/method can generate the required format. Figuring where/how you will do your writing affects what/how you use upstream tools. Don’t assume (ahead of knowing) that a single tool can do everything in preparing your thesis. The different tools in this pace exist with good reason.
Make friends with your reference manager—or pick one and use it—as setting that up correctly will save much proofing time close to submission. Both free (e.g. Zotero, Mendeley, etc.) and pay-for (Bookends, etc.) are available; free is not always better but we all have different budgets, plus getting an RM you enjoy using trumps cost, IMO (it will be your friend for a long while. I’ve learned to never trust citation info from papers until I’ve cited it at publication source; even primary publishers don’t proof the citation. IOW, getting a reference into your RM, is only part of the process. From experience, I learned that a little time at initial ingestion to the RM saves hassle later: e.g. checking, my RM (Bookends) library now has c.20 queries just to spot/fix poor source citation data. I think this is more easily done in an RM than in Tinderbox, given the two are easily interlinked.
Where you store and annotate reference documents is very personal. As a starter, a tool like DEVONthink can be very useful for storing/managing digital sources (e.g. PDFs, etc.). Such tools and some RMs (e.g. DEVONthink, Bookends, etc.) offer pseudo protocols allowing you to use web-like links to call info from one research app from another (e.g. from the Displayed Attributes table or $Text in your Tinderbox notes). For apps that don’t offer a pseudo-protocol take a look at Hookmark as a means of making resources linkable.
Which gets us to Tinderbox. If you store/magange research assets and citations outisde Tinderbox the interlinking opportunities mean that you can concentrate on note-taking and analytic thought, the the other information a click/link away and without filing your TBX doc with. Whether or not you write directly from Tinderbox, it becomes your place to think (and journal) your progress/insights.
Likely not an issue in your field but also note any requirements for submitting background data for the dissertation—you supervisor or org’s library can likely help on that. Pertinent here insofar as it might affect your choice/arrangement of apps. In some fields also consider aspects of ethics, anonymising source, etc. and their constraint if any on your tools & process. IOW, you might not be able to keep all you notes in one document, though Tinderbox has a pseudo-protocol so you can still interlink docs if forced to segment your work.
Note, a number of the pay-for apps here offer good discounts in Summer/ End of year (lat June /late Dec) sale of artisanal software. The summer one approaches and can be a time to make you academic tool budget stretch a bit further.
Circling back, I’d look at how—if at all—the final submission format impacts where/how you write and thus how that relates to your citations data, annotations and general note taking. Specialist deep apps, well connected, can be much more productive than a single app even if that seems counter-intuitive.
Last thought, work in this space is highly personal , even if using the same tools. Don’t assume someone else’s process—however impressive—is an immediate fit for your style. Forcing oneself into another’s process, on the untested assumption of gain, can be disappointing. Think through such a process and the needed tools/expertise/approach you don’t have before rushing to adopt a method. Even if not fully adopted, others’ processes can still provide good ideas—borrow liberally!
Best of luck with the dissertation.