These are the simple instructions that I was given when I asked the same question. So thanks to Goobs on a different forum.
1. factory reset
2. install permission app
3. install all necessary apps and set permissions
4. update HU (no more app install available)
No idea why the factory reset, but I did try without it and it didn't work. So you have performed a factory reset and lost all your radio settings, wallpapers etc. Next connect the car to your home wifi or phone hotspot. Then use the installed browser and go to http://www.cmdroid.com
, and you need to down load the Permissions 1.1 app (first listed).
Once this is downloaded go and install it from the download app. Once installed, and this is important delete the app from the download list. Now go back to cmdroid and download what ever app you want. Bear in mind you can only download one at a time and you must delete it from the list after installing before moving on to the next one. I don't know why but it gave me issues when I didn't, most likely because all apps have the same name to make them work.
So you have installed your apps, in this example Waze. Now you run the Honda Permission app, click on the Process Control I think it is called (list of three on the left side it is the middle one). Tap the large + symbol and enter the details:
Process name: com.waze
Package name: com.waze
Auth Type = THIRD_PARTY
App Type = NAVI
VideoOut = OFF
SoundOut = OFF
SoundInterrupt = ON
SoundInterruptMude = ON
LastMode = ON
OomSetPerm = OFF
ProcessKillTarget = OFF
Hit save and away you go. I have not found any settings for Torque so it may just work out of the box. This website has the setting for Waze and Google should you want it. http://kahur.ee/honda-connect/
Now you can update your headunit again, and you are all set.
It is not actually that difficult I did it yesterday and really was blindly poking in the dark but managed it without issue.