Flushing through the upper flush port you should not run the engine and it won't make a difference what position the engine is in . Flushing through the water intake with the muffs you need to run the engine(for my money it should be flushed this why all the time but there are times that's not possible) what I don't know is weather or not having the engine tilted all the way up will do any damage to the engine(my concern would be with the oil circulation)