Several methods can help you feel less confused. Much of it depends on your contractor, if you have one. Some strategies your contractor might use are a job notebook or a white board, according to Tim Faller, owner of Field Training Services, who teaches contractors how to run their projects better.
I especially like the idea of a job notebook where notes are written about everything that happens on the project. The homeowner can write notes for the crews and the crews can write notes for the homeowners. It can also serve as a record of what went down in case the job ends up in arbitration or court. One consultant I spoke with suggested a spiral notebook, rather than a 3-ring notebook, so the pages are not taken out and remain part of the complete record.
The Daily Log above is one Tim developed for supervisors in the field. If you are acting as your own contractor, you might consider something like this to cut down on the confusion.
Also, if you are running your own project, you might check out Tim's book, The Lead Carpenter Handbook: The Complete Hands-on Guide To Successful Job-site Management. The book is aimed toward professional lead carpenters, which are a hybrid carpenter-supervisor, but you might find some wisdom here on making your project run more smoothly.