Here's what we know so far, and unfortunately it's not all good news. We'll update this post with any additional information we discover.
Skyrim and Skyrim Special Edition are two separate games
You probably know this one, but just in case: if you own Skyrim and its expansions, you'll get Skyrim Special Edition for free, and you don't need to worry about Skyrim SE overwriting or replacing your original copy of Skyrim.
They are two completely separate games. If you have saved games and installed mods for Skyrim, you will still be able to play them with your original copy of Skyrim after the Special Edition appears.
Existing unmodified saved games can be used with Skyrim SE
If you've got saved games from the original Skyrim, you can use them with Skyrim SE. According to an email from Bethesda, it's just a matter of copying and pasting the files:
"Existing save games from the original PC game will work in the PC version of Skyrim Special Edition. Simply copy your old saves from My Games/Skyrim to My Games/Skyrim Special Edition."
So, you'll be able to pick up in the Special Edition right where you left off in the original. This is only for unmodded saved games, though, and here comes the bad news.
Modded saved games most likely won't work at all with Skyrim SE
We haven't had a chance to test this yet (while we have review code for Skyrim SE, we can't play it until the actual launch time), but our understanding is that existing modded saves—that is, saved games in which you used mods for the original Skyrim—won't work at all with Skyrim SE.
Bethesda tells us this in their email:
"Only use original saves that have never been used with mods. Do not use your original saved game if this error appears when you load it in Skyrim Special Edition: This save relies on content that is no longer present."
I've been speaking with Dave Talamas, Community Manager of Nexus Mods today, and he's also pretty doubtful modded saves will work:
"Unfortunately, we haven't had enough internal testing to give you a definitive answer on modded save file compatibility. According to our community of mod authors however, the general consensus regarding compatibility of modded saves is a resounding 'no.' Though there is a remote chance that very particular save files which only depend on mods which have a SSE equivalent installed may work, this will not be relevant to the vast majority of mod users because their modded files will have one or more dependencies with a currently incompatible mod.
"Our advice for mod users is to expect to start fresh when it comes to playing SSE."
Skyrim SE versions of SkyUI and Skyrim Script Extender may take a while to appear
Skyrim Script Extender is a tool many mods rely on, as it expands both scripting capabilities and functionality for mods. Thing is, SKSE was created for the 32 bit Skyrim, and Skyrim Special Edition is 64 bit, meaning the current version of SKSE won't work with the Special Edition.
SkyUI, one of the best and most popular mods for Skyrim, and a mod that many other mods require for configuration, depends on SKSE to work. So, until there's a version of SKSE for the 64 bit version, there won't be a workable version of SkyUI for Skyrim SE.
I asked Dave if he knew the current status of these two incredibly important mods, and he confirmed that SKSE is being actively worked on to support Skyrim SE, though he doesn't know how long it might take.
"The same can be said for SkyUI as it's dependent on SKSE in its current state," Dave said. "A big loss of not having SkyUI as you may know is the loss of in-game mod configuration. So, mod authors are likely to adapt with more rudimentary schemes to allow for in-game mod configuration (such as activating a book), until both are completed."
Update: Dave clarified things a bit further in regards to SkyUI, saying: "...while the SKSE team have confirmed their interest in continuing their work with SSE, the SkyUI developers on the other-hand have not confirmed, but they have expressed interest in collaborating with others who may carry the torch, so-to-speak."
There are some mods for Skyrim SE already
Since Skyrim and Skyrim SE are two different games, modders who post their Skyrim Mods on Nexus Mods need to essentially create duplicates of their work. Many are busy doing this—and Nexus Mods is making this process as easy as possible for them—and some modders who had access to the Skyrim SE beta test already have their mods up on the new Special Edition Nexus page.
The Nexus Mods page for Skyrim SE is right here, so you can see what's currently available. Thankfully, prolific modder Arthmoor has a number of his mods ready to go, including an Unofficial Skyrim Special Edition Patch, which like its predecessor, will fix a number of bugs that were present in the original Skyrim and have been carried over to the Special Edition.
Nexus Mod Manager now supports Skyrim SE
Updated: If, like me, you use Nexus Mod Manager, the Nexus Mods tool for managing your mods, it now supports Skyrim Special Edition.