What I've done in approaching them is to try to approach it like thematic seasons. I find it works well both because that's the format I'm used to with the TV series and because that's how the 'main ranges' later on go.
I know that there's a lot of prose and comics that I'm skipping, but there's something nicely 'authentic' about being able to hear Paul McGann speaking in the role.
I think I've got my chronology nailed down right--I've tried to do a lot of sorting based on Tardis Wikia articles, sticking one-off stories in their appropriate spots relative to the regular 'seasons.' And obviously there's plenty of story to tell between the upcoming Dark Eyes stories and the 50th minisode. But hey, it works for now