Hi tackindy,
It looks as if your focus is more on continuous running as a display layout. I would suggest that you leave the red colored tracks as an expansion project or view it a little differently.
Drop it underneath the main level as a staging area for already made up trains. You enough length on the top of the plan to put in an entrance\exit track and create multiple loops within the width of the main deck.
This allows you have the "actors" exit and return or introduce new "actors". This space where the yard is would make a great place for a logging processing operation or an industry and perhaps a small urban scene.
If you elevate the blue line from the top right to the mountain and down to the bottom right on the peninsula, it would provide your entry\exit to the staging area and provide a good presentation for a train on that line.
I hope your goes smoothly. It can be trying.
