Until recently it was very hard to use multiple mods at once, since the chances were that they'd clash. However this has now become much easier thanks to Sombre's
Mod Compatibility project ([MC]. All the mods listed there work together straightforwardly.
In order to make these packs, I mostly just put all the mods listed on the [MC] page and stuck them together. The only additional work was adjusting some mods so that they were compatible with the [MC] project (and making the preview pictures).
If you want to make your own combinations of nations, all you need to do is get the .dm files for the individual nations, and enable the ones that you want to use. The Mod Compatibility project page is the place to find the individual mod files, although right now it is slightly out of date (since Sombre has not internet at home at the moment). Purely for convenience I'll also attach all the files I used to make the packs to this post.
Now, there's one caveat to all this loveliness of compatible mods: it turns out that there is a limit to the number of mod sprites that dom3 will load at once. If you try to get it to load more then it will crash.
Pack 1 is reasonably close to the limit - you can enable Pack 1, CBM and Holy War Lesser Edition at the same time, but if you add much else it will crash. Pack 2 has a bit more space, so for example you could easily have 1 or two Warhammer nations enabled at the same time as Pack 1. Ultimately if you want to combine bits of the two packs, along with other mods, you're probably better using the individual nation mods rather than these packs. These packs are meant to be a starting point, not a finishing point.