How did the alpha trolls/pre scratch trolls scratch their session and then like became ancestors? I'm still confused on that. Also, how could they have been in the dream bubbles if karkat did the ectobiology stuff?

They scratched their session and normally when a session is scratched you cease to exist but Meenah decided to blow them up before the scratch was complete so they became ghosts instead. 

When a scratch is initiated the meteors headed to Alternia through Skaia’s portals were switched and they were sent to a time way before Karkat’s team was born. They grew up to become the ancestral figures to Karkat and his group.