Is Maggin getting money from the use of Superboy Prime
This just confuses things. I believe Maggin's creation falls under the "work for hire" category, so he got paid to make a comic, and doesn't have rights to the future use of the character. But as Siegels have the rights to Superboy, I believe they have the rights to Superboy Prime.
From what I remember, back in the 40s they ruled that Superboy and Superman were two separate creations, and that Superboy infringed on Siegel's creation. From that line of reasoning, anything derivative of Superboy (Superboy Prime, the Conner Superboy, etc.) also should be in their hands now.
Lana, Lex, and other characters that were later created in the Superboy series are separate issues, and the Siegels don't have rights to them. However, the jury may use them as contextual evidence to decide that Smallville is truly about Superboy.
Regarding the future of things, and the Superboy DVD, I believe the Siegels have the rights to any use of Superboy. If we were to date it as anything created post-2004, that would mean you would have in a sense two copywrites, with DC allowed to publish Superboy archives and such. I think they have the entire rights, but since most of the Superboy $ is in Smallville, they are focusing there first. Once that is decided I think what needs to happen next is either selling the rights back to DC...again...or arguing over percentage of back/future profits.