The only DS emulator is 3desmume, however it's not what you're looking for - you probably want a virtualizer (nds-bootstrap) and a launcher for it (like TWLoader or DSiMenu++ or individual game forwarders), all of which are already well discussed in existing topics (and nothing really beats yet the proven compatibility of a flashcard)
In the TROOP database, select which enemy you wish to have join the fight and insert them into the scene like you would any other enemy. Right click them and select "appear halfway". Then down below in the events panel, set a conditional event for when your main enemy hits a specific %hp and select the "Enemy Appear..." command on page 3. Then select the enemy you wish to appear!