Chicago or APA for draft manuscript?
My main tip would be to use a reference manager that automates the task of formatting references. There are many to choose from. But any good tool should make it fairly trivial to move between author-date format to numbered format. Good tools should also come with a wide range of tools for customising the look and feel of your references. Personally, I use Endnote and it works well for my workflow with MS Word. If you use LaTeX, then you'd want something that works better with BibTeX. That said, I think the big thing is that you get to know the features of your reference manager so you can use it effectively.
In terms of what reference format to adopt, I'd go with the format required by where you plan to submit the work. If it's a thesis, then follow any rules provided by your department. But commonly with PhDs, the format is up to you. In that case, you'd usually adopt the convention (or one of the conventions) of your discipline.