LED module design considerations for an aluminium board
As for Software, I do not know an answer. If you do not have any optics above the board, it really shouldn't matter that much. Just try to distribute them evenly. 

As I. Wolfe already stated, your PCB manufacturer is your friend, talk to him. Out of personal experience, you should try to be as minimalistic as possible with aluminium PCBs. Thru-Hole contacts on an alu board cost a fortune. If possible, keep it on one layer (like in your example photo).

PS: if you have to fix your board with screws, be very careful with conducting lines around those screw- holes. The process of screwing will scratch the solder resist paint away and may result in unwanted short-connections between traces and the aluminium core.