for MOST pontoons, up is the only safe way. You need at a minimum of about a foot under the skeg to be safe. On my pontoon, I can't even lower the motor down all the way while on the trailer.
Depends on your trailer - As long as you have enough clearance between your lowest part (skeg) of your motor & the road fine---
I have a pontoon with a centerlift trailor & i just raise it & rest it on the uppermost "trim" position - doubt i even have to do that but -----