As far as Dragonmarks go, they are complicated insofar as a good way to integrate them into the mechanics while maintaining balance.
I would imagine a good way to deal with them might be to make them feats, as Keith suggested, Lesser Dragonmark, Greater Dragonmark, etc. But that makes humans the only ones to get dragonmarks before level 4. Integrating them into backgrounds makes sense, but pushes backgrounds into game balance territory... everyone would be dragonmarked just because it was so much more beneficial.
My suggestion would be to make general Backrounds for being a Dragonmarked House Member. And then use feats for the lesser/greater etc dragonmarks... with the background allowing one special caveat....
Background Dragonmarked House Member
You are a member of a chosen Dragonmarked house. You are accepted as a member of that house and gain advantage on all social checks with member of that house. etc. etc. You are also able to select Dragonmarked feats (without this background characters can only select aberrant dragonmarked feats). Non-human races who wish to start with a dragonmark at level 1 may choose to ignore all racial ability score increases and instead select the lesser dragonmark feat.
For example, John is playing a High Elf he wishes to be in House Phailarn. Normally a High Elf starts play with a +2 bonus to Dexterity and a +1 bonus to Intelligence, however, John wishes to start play with a dragonmark, so he takes the Dragonmarked House (Phailarn) background and chooses to ignore the base ability score increases at character creation and instead start with the Lesser Dragonmark (Phailarn) feat.