I wouldn't worry too much about hitting the drain tubes. It looks like they are soft enough that they could handle being crushed, as long as it is not raining. If that does not work, just pull them out of the holes in the bed. If you are worried about shearing them off at the bed with the plywood, put a couple of 2 X 4s under the plywood.
By the way, if you have not seen this neat accessory for carrying long items check out
Useful accessory for trailer hitch