One challenge is getting the characterizations right. The Runaways have a very distinct group dynamic, and Cloak & Dagger have their own relationship and personalities. If not done well, it can seem like the characters are just out of place. For example, Gert's scientific mind and her relationship with Old Lace need to be accurately portrayed along with Cloak's brooding nature.
One great 'Runaways and Cloak & Dagger' crossover fanfiction is 'The Meeting of Two Worlds' on FanFiction.net. It has an interesting plot where the two groups accidentally cross paths during a magical event in New York. The characters' interactions are well - written, especially Nico and Tandy's, as they both have powers related to the dark and light aspects.
Overall, Cloak and Dagger stays somewhat true to the comics. Some characters and plotlines are adapted, while others are changed for better storytelling in the TV format. There are additions and omissions, but the core essence remains.
The fate of Cloak or Dagger varies across different comic runs. Sometimes they survive intense situations, while in others, their storylines might take a tragic turn and result in their deaths.