A. Moisture from the humidifier travels downwards due to the natural weight of water. That's why most humidifiers are placed under the lid. However, when a top tray is involved a good way to ensure you get proper humidification below the top tray is to place a jar of humidity crystals (see photo) on the bottom. The evaporation from the jar mixed with the downward flow of air from the top should help give you a better overall RH (relative humidity).

Regarding the positioning of your cigars: Try to keep some space between the cigars for additional airflow. What side they're lying on is not all that relevant. Often with a high capacity humidor, it helps to have a fan to maintain good air circulation. Based on the size of your humidor, a Cigar Oasis XL Plus would be a good solution, but I wouldn't spend the $ unless you felt the circulation was causing serious problems with your cigars.