The community has made serious strides in modding the Souls games. However, as a whole, the games are not mod-friendly. There's no one-size-fits-all SDK, and each aspect of the game has a different tool for modding it (some don’t even have tools). The recommended steps for beginners are:

1. Read the Formats article to get a background.
2. Go through some tutorials, especially the ones in the beginner section.
3. Be aware of the other resources in this wiki, especially the reference material for each game.
4. If you are stuck, confused, or don't know how to proceed, ask for help in the appropriate channel in the Souls Modding Discord (?ServerName?).

There are several hurdles involved with combining multiple mods that edit game files. The leading issue is that there is no concept of “load order” in the souls games, so any file that changes something with the game will completely overwrite similar things. Many files that are modded are one big super file such as the regulation.bin, which contains all the in-game parameter data, so any mod that touches this whatsoever will be naturally incompatible with other mods that also touch it. In some situations, it is possible to manually compare and join the two files yourself, usually with extreme difficulty. If you want to still walk the merging path, there are a few dedicated tutorials in the Tutorial section located here.

Generally yes, the game checks your save file for invalid data, and these checks can be triggered by the vast majority of mods. In some situations, visual only mods will not cause problems, but should still be used cautiously. Mods, especially when used online, qualify as cheating, and are against the Terms and Conditions. Use a system such as ModEngine2 to simplify playing mods and doing so offline in the process.

Whenever you unpack a game archive with WitchyBND, and then edit or put a file inside that unpacked folder, you need to use WitchyBND again on the folder to repack it back so it can be read. Also, if you added a file, you will need to edit the .xml file that WitchyBND created to include the new file in the list of entries, or else it gets ignored when you repack.