I use both of the Genos midi ports at the same time. And, yes it can be a bit confusing. Plus there is a hidden setting on the usb hardware driver for Genos. If you open it up in control panel there is a midi thru option.
The Genos is an odd duck. The way the midi works is strange. Every keyboard I have ever seen... the midi in has the same channels out on the port. Not the Genos.
Midi-1 Genos in is normal. Everything played in will play normally. However, what gets recorded from Midi-1 is everything that you play on the arranger. And Midi-2 is just the opposite. What you play in reaper to Midi-2 Genos in is set to play in the arranger.
Everything is completely configurable in the Genos, however. In order to get the Genos to play both midis you may have to do one reassignment. The input from Reaper thru Midi-2 to Genos in for the keybed gives weird results. Perhaps because the keybed has splits, auto chording, AI settings, etc.
There are extra channels that are available for mapping. I decided to pretty much mirror Midi-2 in and Midi-1 out in the Genos settings. I do not have thru enabled in the control panel for the usb driver.
All my midi is set up through Reaper using a usb printer cable into the Genos with both midi ports enabled.
The Genos has 128 polyphony on each port for 256 total polyphony with both ports in use.