How can I load multiple paths into the workspace during docker run?
You can use Docker volume mounts at run time.  For example:

$ mkdir -p app/src logs
$ touch app/src/foo.c logs/bar.txt
$ docker run --rm -v $PWD/app:/app -v $PWD/logs:/app/logs alpine ls -l /app /app/src /app/logs
/app:
total 8
drwxr-xr-x    2 1000     1000          4096 May  6 23:33 logs
drwxr-xr-x    2 1000     1000          4096 May  6 23:33 src

/app/logs:
total 0
-rw-r--r--    1 1000     1000             0 May  6 23:33 bar.txt

/app/src:
total 0
-rw-r--r--    1 1000     1000             0 May  6 23:33 foo.c


This mounts two directories on the host into the docker container.  Notice in this example that inside the container, they are mount on inside the other.