Creating a critical edition is a complex process, and the software supporting it is not for the faint of heart. There are several different approaches, not mutually compatible, and you need to think carefully about the final product and its audience before deciding on a working method.
If you are interested in producing a digital or print–digital hybrid edition, a peer-reviewed environment for publishing your work finally emerged in early 2018, if your source is in Latin. The Society for Classical Studies, Mediaeval Academy of America, and Renaissance Society of America are launching the Digital Latin Library. They are taking texts of any length, and both working and full critical editions, optionally with translations. The Mediaeval Academy will also consider book-length texts for co-publication with the University of Toronto Press. All this is exactly what scholars have been asking for, and has the potential to go beyond what a print edition can normally do. The underlying mechanism is the Text Encoding Initiative (TEI), a set of guidelines developed since the 1980s, but this seems to be the first serious publication project using it. (For shorter texts, the Scholarly Editing journal remains an option, taking texts in any language.) There are also scripts available for typesetting TEI using LaTeX, as demonstrated in the TEI Critical Apparatus Toolbox. This is still a shifting area, but there is much that looks promising. I have written a post on setting up software to work with TEI for the Digital Latin Library.
If you’re producing a printed edition, Classical Text Editor (CTE) offers the only software for creating a critical edition with a graphical interface, imitating older versions of Microsoft Word. Its primary strength is in typesetting a traditional critical edition, and the results are very good, allowing for attention to various typographical niceties that many publishers have ignored for the last few decades. Its author, Stefan Hagel, is extremely responsive. It is possible to achieve excellent results using it, and relatively quickly. There is some support for creating digital editions, but this aspect remains underdeveloped – entirely due to lack of demand, according to Dr Hagel. CTE is Windows-only, but it’s possible with some caveats to install it on a Mac.
Before using CTE for a new edition, make sure that you have a statement from your publisher, in writing, that they will accept your submission in CTE format. The CSEL series supports it, and Corpus Christianorum will accept CTE files with advance permission. The author guidelines for prominent series such as Oxford Medieval Texts, the Dumbarton Oaks Medieval Library, and Dallas Medieval Texts all ask specifically for Microsoft Word files. The production process in converting a Word text into a critical edition is laborious and error-prone: essentially unchanged from that described in M.L. West’s Textual Criticism and Editorial Technique (Stuttgart, 1973).
If you need to produce a critical apparatus on your own (either for a publisher that requires camera-ready submission or for a thesis), the next most usable option is critical edition typesetting with LaTeX. LaTeX edges out CTE in its typesetting quality through its implementation of the Knuth–Plass line breaking algorithm; combined with the Microtype package, this produces the best automatic paragraph composition available anywhere. The Reledmac package for typesetting a critical apparatus and parallel text is in active development. Many publishers use LaTeX behind the scenes after taking your Microsoft Word file, and are often willing to take direct submissions in this format on request. LaTeX was designed in the 1980s, however, and it can be daunting to learn if you are not familiar with it.
There is, in short, no perfect program for publishing a premodern primary source – at the moment, we have barely progressed since the 1990s, but there is hope for future improvement.