I upgraded from SXOS 2.8 and Emunand 8.1.0 also and it went with out a hitch.
I have my SD card formatted to exFat (because I don't want to deal with splitting large files) and run Emunand in hidden partition. Your set up may differ though I recommend exFat.
1. Make sure you're using Choidujour 1.02 and place the .nro file at the root of your SD card.
2. Create a folder at the root of your SD card called firmware...or anything you want really....and extract the 9.01 firmware to it.
3. Boot SXOS 2.8 (do not upgrade your boot.dat to 2.9.2 yet) and run ChoidujourNX v1.02. Once running, choose the folder you extracted the firmware to. When you see a bunch of nca files on your screen, touch the "Choose" button at the bottom of the screen.
4. On the next screen, you will have 2 buttons....choose the exFat option.
5. Once the new firmware has been analyzed, choose the "Select Firmware" button. Firmware will be verified and extracted. Then press "Start Installation" button.
6. It only takes a minute or two for the new firmware to install. When the yellow bars finish all activity and you see a "Reboot" button at the bottom of screen, you can hit reboot....then hit "Reboot Now" on the next screen.
7. At this point, my Switch wouldn't reboot (I think because the mismatch of firmware 9.0.1 with SXOS 2.8....so I made sure it the Switch was powered down and removed the SD card. I updated the SXOS boot.dat file to 2.9.2 and put it back in the Switch and booted with dongle and jig and it booted right up to 9.0.1 firmware just like it should. Haven't had any issues with it at all.