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For my Yamaha F150 it is basically a requirement according to the manual to use some type of support when trailering if you tilt the motor back. With my setup leaving the motor down, would result in the skeg hitting bumps in the road. I think this would apply to most situations, unless you have a trailer with significant ground clearance. If you have enough clearance, I'd say leaving the motor full down would be the best option. Check your owners manual to see what they say about trailering.
Trailer it up using a transom saver as it is too long to leave down (risk damage on bumpy roads) but if it wouldn't be a clearance issue, I'd tow it straight down.