Current questions and answers regarding the map editor.

For example, I decided to place an Academy town on the map, where archers, crossbowmen, and marksmen will be recruited instead of gargoyles.

Is it okay that the creatures from different factions won't match the game's database?
I've suggested the most optimal method for a general case: cloning the town and modifying the clone to match the ID of a Yeti or Black Knight (if a tier 3 creature is needed, then either a Manticore or a Death Knight). These creatures can be replaced with anything (even from NCF), and we won't have any penalties or minimal impact on other maps.

But, as it turns out, the author needs NCF:

There's a mod that adds the Naga town from Heroes 6 to Heroes 5, based on the Elves, but it's not fully finished. I want to replace the Druids with Water Elementals and maybe the Green Dragons with Water Titans (from the NCF project).

When using NCF, it's enough to replace the ID specifically for NCF with the desired creature's ID, to which the model and other elements will already be linked. Don't forget to change the faction for the desired creatures.
NCF is a mod, and even with an "exe" file, meaning the game will no longer be original (this is for version 3.1). A map with a Naga town without NCF still won't work. If it's a single-player game, then it's fine, but for multiplayer, I wouldn't do that.