I was under the impression those white plastic "liners" were only meant to be used as guides, IE you run your cable all the way through them, then you pull the white plastic "liner" out, and your cable is in the right place.
In terms of the brake one, if your hose won't fit into the "liner" then you'll have to devise a way to connect your brake hose to something else to pull it through the frame. A good idea would be to run a regular brake/gear cable inner through the plastic liner until it comes out the other end, then you can put a few wraps of insulation or duct tape around the last few inches of old brake cable/new brake hose, pull it all the way back through the frame, and it should all work out nicely.