The number of rooms is 1d6 + 1. The "+ 1" room is the section of tunnel itself that passes through the waypoint; there will thus be 1d6 other rooms. Use a d6 with pips, and use the dot pattern as the arrangement of rooms. The bulk of the waypoint can be on either side of the tunnel, but for a waypoint with 7 rooms, I'd have three rooms on either side, with the tunnel running down the middle. There will be alternative access routes between the two sides, either underneath the main tunnel or on bridges across the tunnel.
A two-room waypoint may just be a cave to one side of the main tunnel, possibly on a ledge or in a chasm or pool. Three- and four-room waypoints might be the same, although they might be regular rooms if the inhabitants are intelligence.
You can use the tunnel description roll for the waypoint, too. Certainly, the d4 roll could be used to determine the general class of monster:
- Earthy: Construct (golem, juggernaut, animated dead)
- Watery: Animal, if not actually near water. This means there will be access to food above or in caverns below.
- Airy: Manned outpost.
- Fiery: Spirit of some kind.
Results of 9+ on the description table imply that the waypoint is a rest stop and re-supply center. Some kind of water source will be in one of the rooms; there may also be food stores. Keep in mind that even short tunnels with waypoints may take a day or two of travel, and the longer tunnels are going to take a month or two, so the food supplies may be large, indeed.