What I usually do is start with the "present-day" forms (for whatever value of present day) and then see where I can introduce cool diachronically motivated stuff. Usually that means making up some stuff, coming up with a "reconstruction" that could explain it, change stuff to fit these proto-forms, then decide I want the modern language to be different and changing the proto-forms accordingly, and so on. I'm not sure I have a really good example of this anywhere — I'm pretty terrible at publishing my stuff — but most of my conlangs change wildly until their prehistory is mostly clear, and then they kind of settle down.