They never really went in-depth about the Time War- I always just figured it was tantamount to establishing a bubble universe where all the fighting of the Time War got placed. It's very confusing.
Meta-time is definitely a thing in the Who universe though- things are constantly changing as we go further along the Doctor's personal time-stream. The Silence certainly weren't around when, say, Tom Baker was doing the rounds, for example.
This. Time changes and stuff happens weird all over the place. There are issues everywhere. For instance, in Evolution of the Daleks, Caan Temporal Shifts - in Journey's End we learn that the trauma of watching his allies slay each other and the knowledge of being the last took him right into the Time War. He saved Davros, and that led to the Earth getting stolen - that ended up being in 2008 in Who-universe time.
All that fits, but... in Last of the Time Lords, a year passes. Everything is reset at the end, but in the Martha/Master universe of the 'lost year' the Daleks never take the earth or invade. (Incidentally, how cool would that have been in a sense? Not enough time in an episode for that, mind.) Was this because of the changes The Master caused? It's mentioned in passing that Earth has been quarantined as a dying planet by other species, but that wouldn't bother the Daleks, would it? It's hard to tell, really. Wibbly wobbly and all that.
The Silence probably weren't around during the Baker era (but of course Moffat could argue they were thanks to the memory wipe ability) - I mean, you can argue they "Popped" into existence at a point, retroactively added into history thanks to The Doctor's exploits.
There's probably certain points where when he changes things you can call them turning points, too. I always think The Waters of Mars could be regarded as a point like that, as he so rarely changes "big" things like that. How much else changed from the 'established' time line when he saved those people?
Probably best not to think about it, really. Mental timeline. It's for this reason I think the time travel paradox stuff is best left enclosed in single stories rather than sprawling out all over the show. In this I think River was a bad idea. It's too much for the kids and for a lot of the casual viewers and just sends the fan base cross-eyed as they try to work it out.