When my group is done with the Enemy Within (3ed version) I'm planning on playing through The Thousand Thrones. The players will create new characters, but I still want some connection to previous campaigns. For example before the new Enemy Within we played though the old Enemy Within, and I let things that from that campaign influence the new one. And I planted some seeds in the old Enemy Within to forshadow some of the stuff in the new one. For example the player characters in the old Enemy Within were part of the rescue of Adele with Baerfaust etc.

I'd like to have a similar approach when we transition to TTT. Anyone who played through TTT and maybe even the new (and old?) Enemy Within campaign? Any thoughts on how to integrate the adventures would be appreciated

I was thinking the same, TTT was to follow after Enemy Within. I may be mistaken, but isn't 2nd edition timeline after 3rd edition timeline? The war mentioned at the start of TTT is the same as the one that starts in EW 3rd edition?

Yes, but I have ignored official timelines to link the adventures. So certainly it's the same war, but I will still set the events of TTT after TEW. While the players will have new characters I still want them to feel that their old characters mattered and changed the world in some sense. So I try to forshadow events for TTT while playing TEW and the other way around. For example I change NPCs in the adventure so they match charaters the players (not characters) previously met.

TTT is pretty firmly set after the Chaos Incursion. You could modify the locations and events to occur during the Chaos Incursion instead, but a lot of the atmosphere would feel wrong.

Also, don't forget the TTT Expansions: http://www.liberfanatica.net/TTT.html