Creatures Caves

Hey there, nice to see you! I am not good at smalltalk, so let's get to your questions right away:

1) Generally speaking things that were made for either game will work well in docked worlds. Most C3 downloads are not compatible with DS because they are injected into a fixed space, e.g. the desert. Due to being docked though, those spaces are available again and hence it is safe to use things.
Most DS agents are not compatible with C3, due to DS using a slightly newer version of the engine, so some commands are not available in C3 standalone. Again, this is no problem, as docked worlds also use the newer DS engine.
So overall there is very few agents which are compatible with just one game, but not with the docked version, but those usually explicitely say so somewhere in the description or the readme. Terra Reborn for example overlaps with the Norn Terrarium and hence only should be used in DS-only worlds.

2) As long as you work in your install folder where most of the game files are, she should "work". She is kinda glitchy herself, so be prepared for a mess, even after proper installation. I think there's also a DS version somewhere flying around, which you should get instead when working with docked worlds.

3) Most of these crashes relate to the game not being "prepared" and simply missing some stuff. The two most important things are
A) bibble (i.e. the gibberish like "eem flib dat" that babies speak) cuz the game has none defined for geats.
B) Voices. Creatures need voice files for their audible communication. Those are missing as well.
I made a little patch for the bibble part once, but IDK if there is a standalone voice patch anywhere. The easier solution would be to skip that and instead directly install Ghosthande's Gaius breed. They come with both, the bibble and the voices. (optional Gaius extras here, here and here)
After being done with this primary patching, there is still one liiiiiittle issue. It is generally known as the "wasteland glitch". It causes areas inhabited by more than one geat at once to eventually turn into empty airspace. Soil is made infertile, causing most plants to die off, water turns to air. There have been speculations for possible workarounds, but no practical fix yet. If you wanna keep geats somewhere, use a room that is infertile anyways (like the bridge area of C3 or Random's Room) or accept the fact that your room of choice will soon be devastated.

4) Oh god, tons! the new CFF for example, an improved version of the famous CFE, Garden Box, Magic Words.... I think I'll leave this part to someone else XD