After creating a mod-pack, one such mod you can add for Pokémon Mystery Dungeon: Blue Rescue Team is the Starter Mod, a modification that changes the available starters you can use.
On the New Project window, choose "Starter Mod" in the drop-down, and fill in the name with something that makes sense. Then click OK.
Expand the project you just created and open "Starter Pokemon". You can do this either by double-clicking or by right-clicking and clicking Open.
Edit things to your liking. You should see something that looks like this:
For the purpose of this tutorial, we'll do this:
Click File -> Save -> Save File. Until issue #73 is resolved, there won't be an asterisk before or after saving.
If you try it out, you should see the Pokemon you chose.
Observe the lack of the portraits. When editing EoS ROMs, you can create a project that takes care of that. That is not the case for Blue Rescue Team. The file format is understood, and we can substitute the portraits. However, we can't currently get the game to use the substituted portraits. This may be the side effect of hard-coding, but what exactly controls this is unknown.