Garrett,
First, I like your design, it will be interesting to watch the train weave its way thru the layout.
But ...
It is possible to run two conventional engines heading your consists without worry of them running into each other by using a “Block Section” and an “Isolated Outside Rail Section”. Using two 6-12069 Fastrack Block Sections with the jumper wires connecting the outside rails removed and using 6-12029 Accessory Activator Pack. Connect the isolated rail to either of the outside rails located between the Block Sections. Thus when the moving train passes thru the Accessory Activator Pack section, the electrical connection is made to start the train which is stopped in the Block section. A couple of things to keep in mind are the train in the Block section must be stopped before the train traveling going thru the Accessory Activator Pack section and the Block section must be long enough to stop the train inside the Block section. This link to a youtube video, https://www.youtube.com/watch?v=UQTH5fnVOH8, shows my old Christmas Layout where the upper level trains Stop and Start.
For consideration and if you decide to run one train, I would suggest combining the straight lengths into one and installing two turnouts. This will add interest to the layout as the train will traverse each end loop in a different direction each time it approaches a turnout. This is due the non-derailing feature of the turnouts. I have included simplified RRTrack design.
