Quote from @Garfield M.:
I cant tell by the post how many gas meters and eletric meters there are. Just because it has two furnaces doesn't mean it has two meters. This may be the reason why the previous owner decided to put both thermostats on lockboxes. If there's only one gas meter then you'll just have to do gas included in rent.
If you have two gas meters and two electric meters for the building with unit 1 and garden on same gas/electric meter with the same furnace then I'd do utilities included include in rent for unit 1 and garden.
You can remove lockboxes and replace with modern thermostat with a programmable password. Assuming unit 1 and garden are on same furnace, you can also put a remote sensor in garden unit so you have a way of knowing that garden unit is warm (assuming there is no thermostat in garden unit). You'll want to be sure you keep that unit warm and the tenant happy so 311 is never called for your garden unit.
@Garfield M thanks for the info. For clarity, 3 electric meters (unit 1 and basement/unit 2/Common area) 2 gas meters (unit 1 and basement-same furnace/Unit 2) garden unit actually has a thermostat as well with lockbox. Appreciate the insight on keeping basement tenant happy. Just had a troublesome one that I had to remove!