The best way I have been able to do this is to write a book as I am doing my research. I organize an outline for the ancestors, fill in the details I can find as paragraphs, and pretty much have a footnote (or sometimes two) with every sentence with a source.

For a particularly tricky ancestor, it will start as just a list of sources or leads in roughly chronological order. I work through and try to form these sources into narrative paragraphs as I piece together what is accurate, how they are connected to children/parents/spouses/etc. In some cases, I disprove other people's unsupported theories, and in some cases I present a case for my own conclusions, noting any ambiguity or uncertainty.

I then update my primary tree (on Ancestry.com) with the results of my research, and link or upload the most important original documents there. At some point, I'll upload PDFs of the chapters to the relevant people's pages.

Is there software that could organize this all and make it easier? I'm not totally sure, but I'd be open to considering it.