Each of the 9 lights has 9 different modes that determine when it will flash. Within each mode, you have the ability to specify values to further customize the light. These are entered as numbers, strings (a sequence of letters and numbers), or booleans (values that are either true or false, corresponding to yes or no) to make the lights appear more technical.
Program 0 (Disabled)
The light will never flash. No options.
Program 1 (Variable Check)
The light will flash when the value of a game variable is outside a certain range or matches a provided string. This mode is the most complicated of the 9, and a guide on how to use it and the other modes can be found here. You can also check the Secret Save File page for a list of variables. Mousing over a light in this mode will show the value of the variable in question.
Program 2 (Inventory Check)
The light will flash if you are running out of inventory space. You can specify which inventory menus will activate the light (weapon, armor, accessory, enhancer, potion, and/or outfit) and how many free spaces you can have left before it should start flashing. Mousing over a light in this mode will show the number of inventory slots you have left on each screen.
Program 3 (Time Check)
The light will flash before it is time to enter The Corruption, THE MEGABOSS's Revenge, and Endless Dungeon. You specify how many minutes before the event the light should flash, and which event you would like warnings for. Mousing over a light in this mode will show how many entries you have left in the day for each raid.
Program 4 (Daily Check)
The light will flash if you have not yet completed one of the daily tasks you specify. These include claiming the reward for a daily quest, free card packs in TukkunFCG, claiming Battle Master's reward, collecting the free bacon or broccoli from Ye Olde Pub and 2012: Ye Olde Pub, entering the Spooky Crypt/Triangle Hideout, entering the Secret Dungeon/Endless Dungeon, clicking the Button, claiming the daily Arcade reward, playing death match in the Stadium, fighting the legendary monster in the TukkunFCG, and if you caught anything in Fishing. You choose which of these you want to get reminders for. Mousing over a light in this mode will show which tasks you have not yet completed for the day.
Program 5 (Limit Check)
The light will flash if you have the maximum possible value of various resources. These include Yellow coins, Green Coins, Blue Coins, Garden Points, Fertilizers, Mega Fertilizers, Pixels, Crafting Materials, Energy Refills, and other things (bacon or broccoli, superior crafting material, unobtainium, and enhancer fragments). You choose which of these you want to get reminders for. Mousing over a light in this mode will show which resources you have at the maximum capacity.
Program 6 (LolMarket Check)
The light will flash if you are able to manipulate demand, the price of a gem is above a certain value, and/or the price of a gem is below a certain value. You specify which of these checks you want to perform, the price at which you want to buy gems (where the price entered is multiplied by the gem level and compared to the buy price), the price at which you want to sell gems, and the highest demand at which you want the buy and sell checks to happen. Mousing over a light in this mode will show gem prices and demands and will let you know if you can manipulate demand.
Program 7 (Garden Check)
The light will flash if your trees will expire before their next harvest, you can use fertilizer again, and/or your seed breeding is complete. You specify which of these checks to perform. Mousing over a light in this mode will show you if breeding is active, incomplete, or complete, how long until you can next use fertilizer, and if your trees are about to expire.
Program 8 (Variable Recording)
The light will flash if a variable you choose increases by a certain amount in a specified time. The purpose of this mode is to let you track changes in the value of a game variable. Like program 1, this is complicated, but details are given in the above guide. Mousing over will show the current value of the variable, the last few values, and the increase from the last reading.