The pipelines are just virtual soundcards that you can use to "bounce" audio through, but don’t actually input/output from/to any actual soundcards.
So it’s correct that you’ll want to use the Juli@ for output, and the input will be from Juli@ if you’re wanting to run the inputs directly into Breakaway…
As far as startup issue… I guess that could be possible if the Juli@ drivers rely on having the mixer/etc loaded for the driver to function fully. Some soundcards are like that, I saw a Behringer someone had a while ago that was like that.
It might be possible to delay the loading of Breakaway by 10 seconds or so, on purpose… if you can find some software that can do that. I would bet someone has created that for this purpose before. 8) Let us know if you find such a software in your searching.