I needed to connect two external monitors to my MacBook Pro and use them with a Windows VM inside Fusion 6. Initially when I connected both, Windows would only recognise one of the external monitors, seemingly dependent on which was connected first.
A communities posting revealed a similar issue along these lines. Essentially the automatic detection of the monitors was not working correctly and the suggestion was to power down the VM and update the VM’s vmx file with the below:
svga.autodetect = "FALSE" svga.numDisplays = "3" svga.vramSize = "134217728" svga.maxWidth = "8192" svga.maxHeight = "4096"
This will turn off the automatic detection of the display limits, and allow the VM to use up to 3 displays. You can change it to 4 if you think you might connect a 4th display (using both Thunderbolt ports and HDMI). The absolute maximum number of supported displays is currently 8.
Powering back on resulted in the two external monitors being available, although it still seems a bit flaky. I eventually settled on powering on the VM with no external monitors connected and then once booted, connecting them in the order I wanted them positioned.