It depends on how complex the project is for me. I don't even split the code up unless it's over 1000 lines, and really there's a lot you can do with 1000 lines in AGK.
I typically create the project and make an initiate function after the main loop, and build the project organically from that - adding globals, constants, and arrays and typed arrays at the start of the init function, and functions piled onto the end of the code any-which-way.
If I know the project is gonna be bigger than 1000 lines, or a substantial portion is reusable, then I will split the code up. This is a no brainer really, but I think that the areas that need a lot of fiddling are better off as separate source files - like if your setting up precise physics, getting things balanced well and making your own functions to put a leash on physics sprites, control limits etc, then you probably don't want to have to do that twice - better to have your own physics source file for sprites, that adapts things to the way you want to work and your own perceived scales.
I always indent and add a brief comment for each function, but I don't comment much unless I really have to - I prefer to get a function working, get it folded so I don't have to look at it's ugly face anymore
I don't do a great deal of planning documents, I go trough a lot of graph paper and note paper as I work, but that tends to be for lists and simple diagrams to help visualise what I'm working on. I can go without design documents, but I need a graph paper pad beside me whenever I work... try and find an A5 graph pad and make it your bible.
I'm not sure what this method is called, it's organic and adapts to the project - lets call it the 'blindfolded guide dog who smells waffles' method.
As for level editors.... really you have the best option in your hands already.... make one that will suffice for several projects, or is easily adaptable to the project at hand. People all work different ways and AppGameKit is no exception... even if there was code available for making platform games for example, you'd still need to adapt it for your own project - it will always do something that is outwith the norm, and editors need to adapt to the project they are part of. A while ago myself and Cliff M started a retro 3D dungeon crawler, each enemy, item, wall texture is 32x32 icon sized images, so I made my own sprite editor for that - but I spent the time making it decent, and now it's a vital tool that I use in several projects.... even proper retro like the Atari ST - when you have all the code you can add support for anything you like.
Moreover, I always consider making the level editor part of the actual game - if I was making a platform game for example, I'd consider polishing the level editor and having it as part of the game, let users design levels like Mario Maker. It's the ideal situation to be able to design a level and test it as you go, it's like developer steroids... let's face it, level design can be tedious and time consuming, I think it's always worth spending an hour or two tidying and improving editors, that time is typically saved later on. Things like undo features are difficult to implement, but damn are they handy - if all you need it to do is save the level with each change, and reload it when you mess up, then do it - the time it will save, the confidence it will give, the mistakes it will mitigate, it's worth it.