To start off with If I'm on webapp1(root collection), and I hover over the Newsfeed it takes me to webapp2(root collection) the Web app provisioned as MySite host. Skydrive and Sites links direct me tohttp://webapp1/my/personnal/user.
The goal here is to keep all MySite content on a separate Content database. How can I get this to work such that there isn't a confusion on where to add apps except tohttp://webapp2.