The biggest, most obvious difference between vanilla and AE is the fact that AE no longer uses the formerly ubiquitous *.emz bundles--*.cos.emz, *.col.emz and *.cmn.emz--around everything. This makes it easier for us to move costumes around within the character folders, as you no longer have to hex edit the files; just rename them and you're all set. It also means we don't have to muck around with the emz indexes, which really served no purpose and were a total hassle to create from scratch, even with Kensou's SF4tool.
Vanilla to AE
This is the easier conversion of the two, and the only tool you need is piecemontee's Asset Explorer (aka SF4 Viewer).
To get started, find the file(s) you wish to convert and open them in the Asset Explorer. I'll be using my Santa Rufus mod (both cos and col files included) as an example.
Once the files are loaded in the Asset Explorer, click the plus signs to expand them to the point that you see the components of the emz bundles, as pictured:
Then, just go down the line selecting each component file and then right-clicking and choosing 'Raw dump' from the context menu:
Once you have the components busted out of the emz containers, you're all set. Easy, eh?
AE to Vanilla
This one's a little more complicated, but not by much. It also uses just one tool, but this time it's Kensou's SF4tool, which greatly simplifies the creation of emz containers and indexes.
So, to get started, collect all of the component files from an AE character (*.obj.emo, *.shd.emo, *.nml.emb and *.bsr for a cos.emz bundle, *.obj.emm and *.col.emb for a col.emz bundle or *.skl.emo, *.skl.emm, *.obj.ema, *.fce.ema, *.cam.ema, *.bac and *.bac for a cmn.emz bundle) and put them in an easily-accessible folder (your Desktop works just fine for now). Again, I'll be using my Santa Rufus mod, which I just converted for AE a few minutes ago.
Next, we'll open Kensou's SF4tool. If your SF4tool folder does not already have a folder in it named 'emz' go ahead and create one now and drag our desired component files into it. This probably goes without saying, but we have to work with the cos and col components separately; you can't just dump them all in there at once.
Now, open SF4tool. It should look like this:
Then, in the big window area on the right that shows your file structure, double-click on the emz folder (the one we just created if it didn't exist, remember?) and click the left-hand button (the one crudely circled in red in my screenshot). It should automatically populate the smaller window area with our component files, like this:
Unfortunately, Kensou's tool doesn't know the appropriate order for our emz bundles, so we'll have to move some of the components around to suit. Just click right into that little window and edit the entries that are there until they're in the right order. You might want to open a normal vanilla file in the Asset Explorer first to see which order things should be in (obj, shd, nml, and bsr for a cos bundle).
Once everything is in order, click on the right-hand button (the one that ends in emb) to bundle everything up. This window should pop up if you did it correctly:
Now, back in your emz directory, you should have a shiny new file named "newpack.emz." Just rename that to match the numbers of the component files (in my case, CHB_01) and to reflect the type of file you just created (cos, col, cmn, etc) and you should be all set.