Here... This might help.
You have a route installed and you want to merge another into it. The two routes are at two different heights. To connect them together, you add some blank baseboards to your original route. At the end of the blank baseboards, you attach the other route you want to merge in.
For the kind of merger you want to do, you'll need to put a good number of boards in and when you lay the track down you'll need to swing the track grade back and forth over sweeping curves to connect both routes together to ensure the grade isn't too steep. Once connected over the blank baseboards, you can grade the landscape, put in some hills, plains, meadows, rivers, highways, towns, etc., to fill in the landscape.
After all is landscaped, the end result should be that is difficult to tell where the routes were merged together. In some ways, this becomes an art all in itself. That route in the distance is the Jay Street Connecting Railroad I merged in with my Enfield and Eastern to make up a section of "Hull".
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