Our Zone 2 (bedroom) doesn't have a Furnace setting. That's how we know our two run together. Change your MODE when in ZONE #2 (flashing) to see if it's set up like ours.
If it shows OFF, COOL, FAN ONLY and FURNACE, then they've changed it since we ordered ours . They will run independently and you can set temperature at 2 different settings. If it has no FURNACE, then it's exactly like ours.
2014 Mobile Suite Estates 38RSB - custom home
2014 F450 KR CC 4x4 ...... his office
2015 Lance 1172 - traveling Motel (solar and generator)
Working Fulltimers since 3/2005