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Take a look distribution.yaml for the format of an existing multi-package repo (e.g. navigation).

1). Correct, all the packages (including metapackages) should be subdirs.

2) bloom-release should generate the correct pull request for you, you just need to make sure your repo is set up correctly.

doc:
  type: git
  url: https://github.com/ros-planning/navigation.git
  version: hydro-devel
release:
  packages:
  - amcl
  - base_local_planner
  - carrot_planner
  - clear_costmap_recovery
  - costmap_2d
  - dwa_local_planner
  - fake_localization
  - global_planner
  - map_server
  - move_base
  - move_base_msgs
  - move_slow_and_clear
  - nav_core
  - navfn
  - navigation
  - robot_pose_ekf
  - rotate_recovery
  - voxel_grid
  tags:
    release: release/hydro/{package}/{version}
  url: https://github.com/ros-gbp/navigation-release.git
  version: 1.11.6-1
source:
  type: git
  url: https://github.com/ros-planning/navigation.git
  version: hydro-devel