You shouldn't need any configuration, mouse should just start working when plugged in. You should be able to use both USB and standard mouse simultaneously and there isn't any need to disable either of them. In fact, if you plug several USB mice they all should work simultaneously too
At least that's how it works with my A1200/SpiderII and MorphOS machines.
If you go to Poseidon/Trident preferences and look the devices list, can you see mouse as HID class? If you double click it, does it say it's mouse interface?
You are right. It detects mouses immediately.
Click devices and look for the second device. It should ve a HID class. If it detects it wrong, I think you can select it yourself. You can also double click the HID device and once again double click the device to configure it further. For example, I had to configure the horizontal wheel of my Logitech G7 gaming mouse because it was not detected.
I tried a usb stick and was able to copy stuff to and from it.
I also plugged a Sony Cybershot and could copy pictures back to my Amiga. Opening those pictures crash the Amiga so I think they were corrupted.
When I connected my Samsung Galaxy S4 (it's possible to choose an older picture transfer protocol), it crashed when I was trying to list the contents using Workbench or Dopus. (on my second try it did not crash and I was able to copy one picture to my Amiga.. That picture froze multiview. On the third try it once again crashed while trying to list the contents and I couldn't list the contents again).