I think I am having a similar issue with <a href="http://aros-exec.org/modules/newbb/viewtopic.php?topic_id=10791&forum=2&post_id=107255#forumpost107255">the Trackman Marble I am using</a>. My guess is that Trident either doesn’t save preferences properly to ENVARC: or AROS doesn’t load them at startup. I wrote a bit more in my thread.

For the game Tower57 the porter Daniel implemented support for dual stick joypads using analogue hack for port 1 and 2 and I configured button 1-7 through port 0 and rest of buttons for port 1. Stick 1 is on port 0 and stick 2 is on port 1.
Little difficult to set up but works very good :)

My problem is that when I insert the USB joypad it shows up and everything seams good but for some reason it seams like the ports are not opened within AROS. What I have to do is to go into the controller in Trident and click use. After that everything is good. Just a little painfull and very confusing for people trying to set up a pad like I did. Took some time before I found out this so would be good if someone could give a tips of how this could be solved with maybe a command I could place in user-startup or maybe it is a trival thing to set as default in Trident to make this user friendly.

Edit: Just as a note this does not a problem when I use a controller normal without the analog hack as for example in MAME or other games but as mentioned the analogue hack is essential for the game Tower57.