It is not a given that history was written by “the victors.” History was written by historians; primary sources were written by those in privileged positions (“the winners”). I have written about this quite a bit, so you might want to peruse the archive. I have also made quite a few posts about historical methodology.
The short answer is that historians look at primary sources only after mastering the era. We know what was happening, who was in power, how power was wielded, etc. Then we look at the document and ask who was writing, what place in society this person held, why they were writing it, who they were writing it for, etc. We then analyze it, or attempt to determine its meaning through the bringing together of our contextual knowledge and our documentary analysis.
Secondly, sources written and concerned with women are most certainly not invisible. For more modern periods there are letters, memoirs, photos diaries, legal documents, etc. For less modern periods there are occasional letters and diaries, writings, law codes, observational literature, religious commentary, and so forth. All of this can help historians understand what women were doing in varying periods.
I can’t really give you an answer more specific than that because there are so many historical periods and so many different types of source material. Every field and subfield have their own sub-methodologies depending upon the available source material.
If you can narrow your query I may be able to give a less generalized response.