http://www.xfilestimeline.net/XFilesSeasonTen.htm
I actually don't like the way they did the layout here. Putting pre-revival comics in with the TV timeline just comes off as messy to me. Like, randomly having an issue of the Season 10 comics after television Season 10 even though you have a timeline for the alternate continuation below.
It'd be better to put them all together as a separate timeline... also, they misunderstood the ending of Conspiracy. Everyone thinks that it erased itself but if you read it through properly, the ending is set in a virus-infected timeline that gets overwritten by them sending information back in time leading to the start of the comic where they avoid the virus. It's clearly in-continuity with the comic continuations to me, which I think are clearly implied to be in-continuity with the revival through a reality reset.