If you sell item #1 if station #1 you should create buy and sell order at this station for this item and bot will be able to count profit. You may not sell anything, but underline upper price with sell order of yours for the bot.
I dont know what is better. If you have more then 2kkk, I would just trade in Jita and forget about hauling of the staff from one region to another. But with less sum you may make better percentage of income if you transport items and sell for 200% of a price in different regions (e.g. in systems near zeroes served as enter to zeroes).